What does "\pdfendlink ended up in different nesting level than \pdfstartlink" mean?

The error message "\pdfendlink ended up on a different page" is usually due to a hyperlink (perhaps a citation, or a URL, or cross-reference) somewhere in your PDF, that's breaking across two page (i.e. starting near the end of one page and end on the next). (Citations are possible culprits.) Unfortunately, the pdflatex engine can't deal with this.

As you continue to write more contents, the texts will move around, and the hyperlinks may end up on the same page after all—so you may see that this error seems to "come and go".

For a temporary workaround, so that you can continue working on your project without getting this error, you can disable hyperlinks in your document by writing \hypersetup{draft} just before your \begin{document}, and comment this out when you've finished all your writing. If you're unlucky enough to encounter this problem again at that point, re-enable the draft, and then go through your PDF to find the possible offender (citations, cross-references, floats at top of pages...), so that you can (hopefully) reword your text to avoid the problem.