This worked for me:
1) Figure out what the broken genre is, and where it goes. For example, I would touch "Rock" and get a list of "Pop".
2) Remove from the device all songs from the targeted genre ("Pop" in my example), while keeping songs that belong to the broken genre ("Rock" in my example). I sync everything, so for me this meant changing to "Selected playlists, ..." and then checking all the genres except the one I didn't want. (Renaming the targeted genre will not work. The songs need to be removed. I found that there seemed to be one song that triggered the bad link.)
3) Use the device to access the broken genre again ("Rock" in my example). It will re-index (this took a few seconds for me) and then display the correct entries for the genre.
4) Repeat steps 1-3 for any other broken genres.
Certainly this is a bug, but these steps allowed me to work around it.