I am beginning to wonder if this is a sync created problem. I checked my main big FTM file that I've been working on for years and updated regularly in since getting FTM 2012. There are no obvious source corruption problems. I've never uploaded that file to Ancestry online.
The file I'm having problems with was one I started a few weeks ago, uploaded and have been synching with changes made in FTM2012 daily. I got an idea to try to delete those troubled citations from the online version and synch. The synch report shows they were deleted but they still exist in FTM2012.