If there is, say:

Game [file inside zip has crc 0]
Game (Beta) [file inside zip has crc 1]

and a new version of a dat file swaps them around:

Game [file inside zip has crc 1]
Game (Beta) [file inside zip has crc 0]

ClrMame gets confused and says that they are both missing instead of renaming them properly. You have to move both files to another directory and do a rebuild to get the right names.