Sorry for the late reply, I thought I had replied to this already.
I have not place a nocite anywhere in the md file. 
This really seems like a wandering bug. I cant say whether 2.11.1 placed all references in the reference list as I didn't test that but it certainly happens when using 2.11.2
What I find very confusing is the fact that pandoc can create a yaml or json from a bib file but can't use external references when compiling a document. All of these files are in the same directory, the mad, bib, json and yaml.
Perhaps the fact that pandoc couldn't find my latex template, which also resides in the same directory, indicates a common issue. Somehow the path is corrupted when compiling a markdown file that calls on secondary files.

On Tuesday, 1 December 2020 at 19:39:21 UTC+1 John MacFarlane wrote:
Andrew Mercer <mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:

> Further update. Adding references to the yaml works but ALL references in
> the yaml are then place in the reference list at the end of the compiled
> document.

Do you have `nocite` in your metadata?

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