I have a book that has pages with footnotes, but the last and only the last one or two footnotes are always broken on my Kindle Paperwhite (Not on any other reader). That means they are treated as links instead of pop-up footnotes.
The structure is roughly this (repeating on each page):

  <span class="sentence">$sentence</span>
  <a href="footnotes.xhtml#first-2-6" id="first-2-6-ref" epub:type="noteref">First</a>
  <a href="footnotes.xhtml#second-2-6" id="second-2-6-ref" epub:type="noteref">Second</a>

And then footnotes.xhtml (again, repeating):

<aside id="first-2-6" epub:type="footnote">
  <a href="chapter.xhtml#first-2-6-ref">First:</a>
  Content of Footnote First
<aside id="second-2-6" epub:type="footnote">
  <a href="chapter.xhtml#second-2-6-ref">Second:</a>
  Content of Footnote Second.

Most strangely, it works if I remove all footnotes of the type First or Second respectively, just not in combination.

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