When doing a repoman scan, it doesn't detect the presence of extra files (not in CVS) or other fluff that repoman commit barfs on. Perhaps repoman commit should be trained to ignore obvious backup files, such as .#foo and foo~ and foo~1.2 (from a killed CVS)?
Not much for making repoman (and by extension, the Manifest) ignore certain files. Either way, try repoman commit --pretend.