Vault uses the CRC32 checksum to detect changes in files which has 4,294,967,296 possible values. This seems like a huge number, but when you consider a system with a million files each with 10 or more versions, the probability of a CRC32 clash becomes highly probable. In addition, some softwares have been known to abuse the CRC32 checksum resulting in frequent duplication.
Currently, when Vault recognizes that the checksum hasn't changed during the check-in process, it cancels the upload without warning to the user. I'd like to suggest that the user instead be prompted with a dialog box that warns the user that the file queued for upload has the same checksum as the existing file in the Vault. This dialog box would give the user the ability to force an upload if desired.
Alternatively, Vault's algorithm could consider the CRC64 instead of the CRC32 or consider both. The CRC64 has 1.8 quintillion possible values.