We had the same problem: duplicate file name or a file name that had an additional number in it (I.E.: serial number should be NCM-1234, but file was named NCM-12324). After checking data cards (first step), checking template used to create these files (2nd step).. we found that this issue was caused by a user making a copy of the existing file and pasting it into one of the folders. This only happens if it is the last file number pulled or if by some chance there is an existing file with the same serialization number as your next one... Either way, user was slapped... we have not had the problem since.
SolidWorks Answer: If the user that is running the Enterprise file template lacks Destroy permission in the target folder, cancelling the template may leave the file it is creating in the folder.
This is a known issue, reported under SPR 398575 "Cancelling a file created by template leaves orphaned file copy if user lacks folder Destroy permission "
Ensure the logged in user have the folder permission destroy. The user does not need destroy permission in any workflow state - so the workflow would prevent delete and destroy of files that have been checked into the vault at least once. The only files that user would be able to destroy (i.e. bypass deleted items) would be files still in users private state, added but not yet checked in. Once checked in, the workflow permissions are required as well.