I'm using v0.13-DEV buildDate: 2014-12-13T10:03:26-06:00. My footnotes are being generated like this:
<sup class="footnote-ref" id="fnref:4e97c4f6dc307e09ab266d7ceea7b3d2:1"><a rel="footnote" href="#fn:4e97c4f6dc307e09ab266d7ceea7b3d2:1">1</a></sup>
<li id="fn:4e97c4f6dc307e09ab266d7ceea7b3d2:1"><p>Footnote reference</p>
<a class="footnote-return" href="#fnref:4e97c4f6dc307e09ab266d7ceea7b3d2:1">↩</a></li>
These links are not working. (Here is an full example.) I suppose it should be clear why they are not, but I don't know if it's path problem or if it's related to the apparently superfluous code generated in the hrefs.