hyperref pdf table of contents messed up (probably bookmarks problem)

The bookmarks are the things in the sidebar. The runaway error probably means that one of your \chapter etc command contains something which breaks when hyperref tries to put it in the bookmark. Inspect the aux and the out file. Perhaps you can find the culprit. Or put \end{document} in the middle of your document and then move it around until you find the point where the error appears.

For those wanting another solution: I found trashing (clearing) the .aux files and re-running LaTeX helped me with the same error.

I think the issue is that my co-author made some edits, and when I pulled them and ran LaTeX, it did an incremental update with some bad info in the .aux files. Clearing them and re-running helped.