I have a similar problem - running Mac OS X Sierra, Word 2016 from Office 365 latest update (15.35).

Got a large document (50,000 words) with a standard table of contents set up to create based on Heading 1 and 2 from styles pane. This all worked fine but now is recognising half the 'normal' styled text in the document as table of contents material - it makes the Document Map completely useless and if I update the toc does the same there.

Any suggestions warmly welcome!