Links in TOC go to the wrong page

If a book, is an Edit > Update Book being done prior to rendering, and if so, are all of these checked?

☑ Update Numbering
☑ Update All Cross-References
☑ Generate TOC, lists, IX

It's my practice to run this update twice before a final render. Any of those updates could cause a change in pagination, leaving the numbering incorrect. Doing it twice increases the odds that the final output will be correct. We might expect FM to detect it, and re-run it internally, but I don't know that this happens.

Suppose the Generate adds one line to the TOC, resulting in a new page, or a page Xref was to p99 but is now p100, spilling some content to a new page.

Are the links working correctly in FM to begin with? You can test by holding down the Ctrl-key as you click on one of the incorrect links.

Did you enable the "Create Named Destination for All Paragraphs" option in the Links tab of your PDF Setup?