Help us understand something, is it still running? If so, shut the source down so as not to cause further issues. The big thing with upgrades is the DB must be inline with the vaults. Not the end of the world but you could end up with missing files or in some cases, extra files that cause issues when writing new data to the vaults. There are standard validation scripts that you can run on vaults or folders which will validate that each file the database says should be there are there and it should be as simple to move in the missing files with the same timestamps. What should have happened is when you did your upgrade, you shutdown the source to freeze it until its complete.
Next question, did you make a complete copy of the vaults from source to target? Or are they using the same location? If it was a copy and source was still running, you might get extra files. It really depends on when the database extract was taken. That is the key part since what is in those vaults need to align. If you took the DB extract and users kept working, the work then did after that point is not in the DB extract so any files they added to the vault are stuck with the source. Adding them to the vault will not help since DB did not have a record of that. Recommend running WContentVerify Tool
