Looking at the markup, I'd guess it is caused by your putting the <sup> tags inside the <a> tags instead of outside them.
You have:
<a class="calibre5" href="part0000.html#end1" id="endref1"><sup class="calibre6">1</sup></a>
change that to
<sup class="calibre6"><a class="calibre5" href="part0000.html#end1" id="endref1">1</a></sup>
And you should be fine.
Presumably the Kindle software cannot handle the former.