When reading an ePub book generated by Pandoc with iBooks for iOS, popup footnotes won't open. Here's why. Pandoc writes the footnotes as:

<a href="#fn1" class="footnoteRef" id="fnref1" epub:type="noteref"><sup>1</sup></a>

When the <sup> tag is inside the <a> tag, popup footnotes break (for that matter, if any tag is inside the <a> tag, the footnote won't work). This is a fairly well documented problem -- here on Github, on the Adobe InDesign forums, or on Liz Castro's website for example. In order for the footnote to properly work in iBooks, the markup should be :

<sup><a href="#fn1" class="footnoteRef" id="fnref1" epub:type="noteref">1</a></sup>

Another tweak would go a long way in improving the reliability and legibility of Pandoc-generated ePubs: allowing the user to specify if the footnotes block should be visible (<section class="footnotes">, good for books designed to be distributed on many plateforms) or not (<aside class="footnotes">, good for books designed to be distributed on the iBooks Store only, or for the iBooks version of the book, as iBooks hides asides by defaults).

Hope it helps!