Update:
After creating an entirely new file and getting the same results mentioned in the op, I finally had the idea of verifying the generated EPUB with EPUB-Checker. I couldn’t find anything wrong with the .idd file so I looked at the generated html. What I ended up finding was a mess.
Endnotes.
The endnotes section of the html looks something like this:
<p class=”Notes_Notes-List-1″><span id=”endnote-037″>1 “My Endnote Text.</span></p>
But the section <span id=”endnote-037″> is often exported like this <span id=”endnote-000”>. Sometimes I would export to EPUB and all the endnote ids would be set to 000, sometimes just a a subset would be set to 000, and sometimes they would all be correct. This explains the random behavior I was seeing. However, even after going in and fixing these errors when viewing the EPUB in iBooks, the endnotes still randomly link to either the correct endnote page, or the page just after the correct page.
Unordered Lists.
I am not yet sure if this is related, but it seems that sometimes Indesign exports the EPUB with incorrect html tags; at least regarding unordered lists. I found at least one unordered list for which the close tag appeared long after the end of the list. This means that everything until the close tag was logically included in the unordered list. Like I said, I have no idea what impact this may or may not have on the issue I am having with the endnotes.