Digging around I found this Symantec knowledge base article http://seer.entsupport.symantec.com/docs/305058.htm
By default EV deletes any temporary files that are older than 24 hours, if you add the registry mentioned in the above article 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.