An issue discussed briefly earlier on this forum (https://groups.google.com/d/topic/pandoc-discuss/IR7nL7lEHpc/discussion) still seems to exist and seems to require a solution at the pandoc-citeproc level. 

Essentially, the problem is that the \hypertarget{ref-soandso} inserted in front of entries in the bibliography has the counterintuitive and obviously undesirable side effect of preventing page breaks between entries--only within them. That is, if you have a reference occupying two lines in the bibliography followed by half a page of single-line items and then another multi-line entry, the resulting PDF will have a page break between the two lines of the first entry followed by simple whitespace for the rest of the page. In other words, it's an absolute refusal to allow the page break to come between "paragraphs" in the bibliography, no matter how much whitespace gets left behind as a result--obviously a ridiculous result.

I'm sure there's a workaround. The solution offered in the discussion linked above was to place this just before the bibliography: 

\let\oldhypertarget\hypertarget

\renewcommand{\hypertarget}[2]{%

    \leavevmode%

    \oldhypertarget{#1}{#2}%

}

<div id=“refs”></div>

Doing so, however, in turn has the unexpected effect of messing with the left alignment of some references--many are still where they should be, while others are indented random amounts. So that's not great either. I'm not sure why \leavevmode is having this effect, if it is, but, again, not acceptable. 

Anyone have a solution to this problem? I'd hesitate to call it a bug, but it is certainly not how things should be.