Sounds like you're having a similar problem as me, this might help.
By default EV deletes any temporary files that are older than 24 hours, if you add the registry mentioned in this Symantec article http://seer.entsupport.symantec.com/docs/305058.htm or Registry_Values.pdf, you can clear them down sooner.
Resolution
Add the following registry keys to delete these types of files.
1. Go to Start | Run on the EV server, type regedit and click OK.
2. Expand HKEY_LOCAL_MACHINE\SOFTWARE\KVS\Enterprise Vault\AdminService.
3. Right-click AdminService key and choose New > String Value.
4. Enter the name DelFileTypes (case sensitive).
5. Double-click on DelFileTypes and enter a list of file types separated by a semi-colon.
For example:
ExchangePerf*.dat;EV$*.*;*.tmp;~DF*.tmp
6. Right-click AdminService key and choose New > DWORD Value.
7. Enter the name DelFilesOlderThanHours (case sensitive).
8. Double-click DelFilesOlderThanHours and enter a decimal value for hours.
NOTE: If the value of DelFilesOlderThanHours is set to zero, all matching files will be deleted immediately, as long as they are not read-only, are directories, or are in use.
9. Restart the Enterprise Vault Admin Service for the changes to take affect.