A system security document I was editing had a problematic table of contents in Word. This was in Word 2010, but my research indicated it can happen in Word 2007, 2003, and very possibly earlier versions as well.
The problem was that I had two blank entries in the table of contents. When I clicked on the links, they led to the entries right below them in the TOC, making them completely extraneous.
To eliminate these phantom whitespace entries, I went to the heading that the blank entries led to. I inserted two blank lines before and after the heading. I then copied the heading to the line above it, then deleted the old heading, then deleted the remaining blank lines.
I then returned to the table of contents, right-clicked, hit “Update Field,” and the table of contents updated properly.