Using the MWE below, I cannot reproduce your issue. (Not even with citations in footnotes `Blah^[@cit, 34-45].` -- something you’ll *really* want to avoid. -- `p999`, BTW, does not work either; just use `999`.)

Did you check whether your `modern-humanities-research-association.csl` is up to date?

~~~
pandoc -s -F pandoc-citeproc -t markdown-citations-markdown_in_html_blocks << EOT

Blah [@cit, 34-45].

Blah [@cit2, 56-67].

Blah [@cit, 67-78].

Blah [@cit2, 78-89].

---
csl: modern-humanities-research-association.csl

references:
- id: cit
  type: book
  author:
  - family: Lastname
    given: Firstname
  issued:
  - year: '2016'
  title: Long title; that could be abbrev
  title-short: Abbrev
  publisher: Fictional
  publisher-place: London
  language: en-en

- id: cit2
  type: book
  author:
  - family: Surname
    given: Firstname
  issued:
  - year: '2016'
  title: Another long title; that could be short
  publisher: Fictional
  publisher-place: London
  language: en-en
...
EOT
~~~


On Sunday, 20 March 2016 22:40:41 UTC, Frank Colcord wrote:
Hi Jesse,

Thanks for your suggestions.

I will have to discuss with my friend writing the dissertation.

It looks as if we still have the same choice (see pdfs version 6 and 7 enclosed).

Version 7 is what led to the original bug report of double commas.

Thanks for your prompt help.

Frank


On 20 March 2016 at 22:01, Jesse Rosenthal <jrose...@jhu.edu> wrote:
The issue, I think, is that you're manually inserting in-text citations
into footnotes, instead of using a CSL style (like chicago-fullnote-*)
that does footnotes automatically. Footnotes or not are a style-specific
decision: if you put them in by hand, you'll get odd results.

That being said, if you really need to do it that way for some reason,
you could probably get away with it by following the format for in-text
citations, like so: `^[@cit [p9999]].

Frank Colcord <fr...-XCqNk0BTMejR7s880joybQ@public.gmane.org> writes:

> [ text/plain ]
> Just reran and it made the pdf.
>
> Same problem.
>
> On 20 March 2016 at 21:48, Frank Colcord <fr...-XCqNk0BTMejR7s880joybQ@public.gmane.org> wrote:
>
>> Hi Jesse,
>>
>> Yes, it could be the csl.
>>
>> When I revert back to my January csl, I don't get the same error.
>> But I don't get anything at all! No pdf.
>>
>> I enclose my January csl.
>>
>> Frank
>>
>>
>>
>> On 20 March 2016 at 21:45, Jesse Rosenthal <jrose...-4GNroTWusrE@public.gmane.org> wrote:
>>
>>> Sorry -- to clarify: I get the same problematic output when I run it
>>> with MHRA. I can't reproduce the pandoc-citeproc error you get below. Is
>>> it possible that you're running it from a different directory, and
>>> you're relative path to the csl file is breaking?
>>>
>>> Frank Colcord <fcol...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
>>>
>>> > [ text/plain ]
>>> > Just realized one of the files I enclosed last time was incorrect.
>>> > I enclose the correct markdown file "DoubleCommaBugv2.txt"
>>> >
>>> > I've now updated pandoc.
>>> >
>>> > pandoc 1.16.0.2
>>> > Compiled with texmath 0.8.4.1, highlighting-kate 0.6.1.
>>> >
>>> > pandoc-citeproc 0.9.1.1
>>> >
>>> > Just downloaded latest version of
>>> > styles-distribution/modern-humanities-research-association.csl
>>> >
>>> > However, I get an error report:
>>> >
>>> > prompt> pandoc DoubleCommaBugv2.txt --toc --variable mainfont="DejaVu
>>> > Serif" --csl=../../csl/modern-humanities-research-association.csl
>>> > --bibliography=DoubleComma.bib --chapters --latex-engine=xelatex -V
>>> > hyphenate=false -V links-as-notes -N -o DoubleComma.pdf
>>> > pandoc-citeproc: ParseError {errorContexts = [], errorMessage = "Failed
>>> > reading: takeWhile1", errorPosition = 51:5}
>>> > pandoc: Error running filter pandoc-citeproc
>>> > Filter returned error status 1
>>> >
>>> > thanks,
>>> >
>>> > Frank
>>> >
>>> >
>>> > On Sunday, March 20, 2016 at 9:05:37 PM UTC, Frank Colcord wrote:
>>> >>
>>> >> Above tests were run using
>>> >>
>>> >> pandoc-citeproc 0.9
>>> >>
>>> >> pandoc 1.16.0.2
>>> >> Compiled with texmath 0.8.4.1, highlighting-kate 0.6.1.
>>> >>
>>> >> I will now update and revert.
>>> >>
>>> >> thanks again
>>> >>
>>> >> Frank
>>> >>
>>> >>
>>> >> On Sunday, March 20, 2016 at 8:30:02 PM UTC, Frank Colcord wrote:
>>> >>>
>>> >>> Of course. I forgot to update everything before I ran those tests.
>>> Last
>>> >>> update was early February. Will revert in an hour when I get home.
>>> >>>
>>> >>> Thanks Frank
>>> >>> On 20 Mar 2016 8:10 p.m., "John MacFarlane" <j...-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org>
>>> wrote:
>>> >>>
>>> >>>> Before we look further, could you also indicate what
>>> >>>> versions of pandoc and pandoc-citeproc you're using?
>>> >>>> Doubled commas used to be common but we've squashed a
>>> >>>> lot of the bugs in recent versions.
>>> >>>>
>>> >>>> +++ Frank Colcord [Mar 20 16 10:25 ]:
>>> >>>>
>>> >>>>>   Hi Everyone,
>>> >>>>>   this is my first post on this forum, after some lurking, so please
>>> >>>>>   forgive me if I make an error.
>>> >>>>>   I'm getting two commas in my footnotes when I would just expect
>>> one.
>>> >>>>>   I've enclosed all the relevant files.
>>> >>>>>   Please let me know if I have missed out some information.
>>> >>>>>   I'd like to know if I have made an error in my files, or if this
>>> is a
>>> >>>>>   bug in Cite Proc or in Pandoc.
>>> >>>>>   I'm happy to file the bug if it is one.
>>> >>>>>   kind regards,
>>> >>>>>   Frank
>>> >>>>>
>>> >>>>>   --
>>> >>>>>   You received this message because you are subscribed to the Google
>>> >>>>>   Groups "pandoc-discuss" group.
>>> >>>>>   To unsubscribe from this group and stop receiving emails from it,
>>> send
>>> >>>>>   an email to [1]pandoc-discus...@googlegroups.com.
>>> >>>>>   To post to this group, send email to
>>> >>>>>   [2]pandoc-...@googlegroups.com.
>>> >>>>>   To view this discussion on the web visit
>>> >>>>>   [3]
>>> >>>>>
>>> https://groups.google.com/d/msgid/pandoc-discuss/929c0871-77ed-4637-
>>> >>>>>   a0bf-506d89f7a71d%40googlegroups.com.
>>> >>>>>   For more options, visit [4]https://groups.google.com/d/optout.
>>> >>>>>
>>> >>>>> References
>>> >>>>>
>>> >>>>>   1. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>>> >>>>>   2. mailto:pandoc-...@googlegroups.com
>>> >>>>>   3.
>>> >>>>>
>>> https://groups.google.com/d/msgid/pandoc-discuss/929c0871-77ed-4637-a0bf-506d89f7a71d@googlegroups.com?utm_medium=email&utm_source=footer
>>> >>>>>   4. https://groups.google.com/d/optout
>>> >>>>>
>>> >>>>
>>> >>>> @book{cit,
>>> >>>>>  location = {{London}},
>>> >>>>>  title = {Long Title; that could be abbrev},
>>> >>>>>  shorttitle = {abbrev},
>>> >>>>>  timestamp = {2016-02-07T14:08:21Z},
>>> >>>>>  langid = {EN-en},
>>> >>>>>  publisher = {{Fictional}},
>>> >>>>>  author = {Lastname,Firstname},
>>> >>>>>  date = {2016}
>>> >>>>> }
>>> >>>>>
>>> >>>>> @book{cit2,
>>> >>>>>  location = {{London}},
>>> >>>>>  title = {Another Long Title; that could be short},
>>> >>>>>  timestamp = {2016-02-07T14:08:21Z},
>>> >>>>>  langid = {EN-en},
>>> >>>>>  publisher = {{Fictional}},
>>> >>>>>  author = {Surname,Firstname},
>>> >>>>>  date = {2016}
>>> >>>>> }
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>
>>> >>>>
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable fontfamily="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-language-association.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V hyphenate=false -V
>>> links-as-notes -N
>>> >>>>> -o LaHarpeCh1-Feb7-4.pdf
>>> >>>>> result:
>>> >>>>> pandoc-citeproc: ParseError {errorContexts = [], errorMessage =
>>> "Failed
>>> >>>>> reading: takeWhile1", errorPosition = 50:5}
>>> >>>>> pandoc: Error running filter pandoc-citeproc
>>> >>>>> Filter returned error status 1
>>> >>>>>
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable fontfamily="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V hyphenate=false -V
>>> links-as-notes -N
>>> >>>>> -o LaHarpeCh1-Feb7-4.pdf
>>> >>>>> result: ok
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable fontfamily="DejaVu Serif"
>>> >>>>> --csl=./csl/chicago-fullnote-bibliography-no-ibid.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V hyphenate=false -V
>>> links-as-notes -N
>>> >>>>> -o LaHarpeCh1-Feb7-5.pdf
>>> >>>>> result:
>>> >>>>> pandoc-citeproc: ParseError {errorContexts = [], errorMessage =
>>> "Failed
>>> >>>>> reading: takeWhile1", errorPosition = 50:5}
>>> >>>>> pandoc: Error running filter pandoc-citeproc
>>> >>>>> Filter returned error status 1
>>> >>>>>
>>> >>>>> take out commas after parker citations
>>> >>>>> pandoc LaHarpeCh1-2016-02-07.txt --toc --variable fontfamily="DejaVu
>>> >>>>> Serif" --csl=./csl/modern-humanities-research-association.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V hyphenate=false -V
>>> links-as-notes -N
>>> >>>>> -o LaHarpeCh1-Feb7-4a.pdf
>>> >>>>> result: ok
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --template=MtemplateQuote.txt
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --chapters
>>> --latex-engine=xelatex -V
>>> >>>>> links-as-notes -N -o LaHarpeCh1-fc9.pdf
>>> >>>>>
>>> >>>>>
>>> >>>>> 15. 17 Jan 2016:
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1-fc-Jan1.txt --toc --variable mainfont="DejaVu
>>> Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association-author-date.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V links-as-notes -N -o
>>> >>>>> LaHarpeCh1-fc-Jan18-2.pdf
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable mainfont="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association-author-date.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V links-as-notes -N -o
>>> >>>>> LaHarpeCh1-fc-Jan18-3.pdf
>>> >>>>>
>>> >>>>> I realized that the csl files might be out of date. They were valid
>>> Oct
>>> >>>>> 2015. I've just downloaded Dec 2015.
>>> >>>>>
>>> >>>>> 16: 17 Jan 2016:
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable mainfont="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association.csl
>>> >>>>> --bibliography=Harpeorganiséemaria-fc.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V links-as-notes -N -o
>>> >>>>> LaHarpeCh1-fc-Jan18-4.pdf
>>> >>>>>
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable mainfont="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association-author-date.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V links-as-notes -N -o
>>> >>>>> LaHarpeCh1-fc-Jan18-5.pdf
>>> >>>>>
>>> >>>>> The new versions of the csl don't sort out the space and comma
>>> issues.
>>> >>>>> So, the author date still looks like the best solution for now.
>>> >>>>>
>>> >>>>> cd Dropbox/LaHarpeOrganisee
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable mainfont="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association-author-date.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V hyphenate=false -V
>>> links-as-notes -N
>>> >>>>> -o LaHarpeCh1-fc-Jan18-6.pdf
>>> >>>>>
>>> >>>>> cd Dropbox/LaHarpeOrganisee
>>> >>>>> pandoc LaHarpeCh1.txt --toc --variable mainfont="DejaVu Serif"
>>> >>>>> --csl=./csl/modern-humanities-research-association.csl
>>> >>>>> --bibliography=Harpeorganiséemaria.bib --template=MtemplateV3.txt
>>> >>>>> --chapters --latex-engine=xelatex -V hyphenate=false -V
>>> links-as-notes -N
>>> >>>>> -o LaHarpeCh1-Feb7-1.pdf
>>> >>>>>
>>> >>>>>
>>> >>>>> ----------------------------------------------
>>> >>>>> blanks in second use of citation
>>> >>>>> ----------------------------------------------
>>> >>>>>
>>> >>>>> Maria: blanks I don’t know about but there is also an extra comma,
>>> as
>>> >>>>> if the forename is missing from the ref. eg. “Barthel, , Title of
>>> book..”
>>> >>>>>
>>> >>>>> Frank: Let me know if you want me to work with you on this.
>>> >>>>> I assume it has to do with the way you've filled in the fields of
>>> >>>>> Zotero. Compare a good citation against this one.
>>> >>>>>
>>> >>>>> Maria:
>>> >>>>>
>>> >>>>> Frank: 17 Jan 2016:
>>> >>>>>
>>> >>>>> I think using the MHRA author date csl has sorted this out as well.
>>> >>>>> Have a look at  "...18-3.pdf" and see if that works for you.
>>> >>>>>
>>> >>>>> Maria: ok
>>> >>>>>
>>> >>>>> Frank 7 Feb: Now that you've decided on author title date, let's
>>> figure
>>> >>>>> out the right citation style and trouble shoot from there.
>>> >>>>>
>>> >>>>> Maria: remove , it the same issue as above.
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>> --
>>> >>>> You received this message because you are subscribed to a topic in
>>> the
>>> >>>> Google Groups "pandoc-discuss" group.
>>> >>>> To unsubscribe from this topic, visit
>>> >>>>
>>> https://groups.google.com/d/topic/pandoc-discuss/IBf4wGbbFhk/unsubscribe
>>> >>>> .
>>> >>>> To unsubscribe from this group and all its topics, send an email to
>>> >>>> pandoc-discus...@googlegroups.com.
>>> >>>> To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
>>> >>>> To view this discussion on the web visit
>>> >>>>
>>> https://groups.google.com/d/msgid/pandoc-discuss/20160320201043.GA916%40MacBook-Air-2.local
>>> >>>> .
>>> >>>> For more options, visit https://groups.google.com/d/optout.
>>> >>>>
>>> >>>
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> Groups "pandoc-discuss" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> an email to pandoc-discus...@googlegroups.com.
>>> > To post to this group, send email to pandoc-...@googlegroups.com.
>>> > To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/pandoc-discuss/c17dbe54-a14e-4ba5-ac9f-1c70e05a51a4%40googlegroups.com
>>> .
>>> > For more options, visit https://groups.google.com/d/optout.
>>> > [ DoubleCommaBugv2.txt: text/plain ]
>>> > This is a test of having the same work^[@cit, p9999] mentioned twice in
>>> the same document.
>>> >
>>> > If there is only one citation in the paper, then it thinks it can
>>> ignore the author altogether, except in the bibliography, so I had to
>>> include another work^[@cit2, p2] which may help.
>>> >
>>> > If I don't put the citations in the footnote style^[@cit, p1000] , the
>>> author names are put in the sentences.
>>> >
>>> > This is a test of having the same work ^[@cit2, p1000] mentioned twice
>>> in the same document.
>>> >
>>> > Here is the command I issued. No pdf template needed.
>>> >
>>> > ```````
>>> > pandoc DoubleCommaBugv2.txt --toc --variable mainfont="DejaVu Serif"
>>> --csl=../../csl/modern-humanities-research-association.csl
>>> --bibliography=DoubleComma.bib --chapters --latex-engine=xelatex -V
>>> hyphenate=false -V links-as-notes -N -o DoubleComma.pdf
>>> > ``````````
>>>
>>
>>
>>
>> --
>> fr...-XCqNk0BTMejR7s880joybQ@public.gmane.org, cell: +447763116793, skype: colcord,
>> if you ever get no response, please send to: fcol...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
>>
>
>
>
> --
> fr...-XCqNk0BTMejR7s880joybQ@public.gmane.org, cell: +447763116793, skype: colcord,
> if you ever get no response, please send to: fcol...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
> [ DoubleComma.pdf: application/pdf ]



--
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if you ever get no response, please send to: fcol...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org

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