It seems that some program checks whether other program opens file with write access and if so, it denies to process the file. Those programs need exclusive write lock. I think after BitTorrent download finish (before seeding over), re-opening files in read-only mode will fix this issue, but it may be dangerous because if data is accidentally modified, the modified data will be uploaded into BitTorrent swarm and the peers received these invalid data must re-download the piece.
Also, I noticed that often aria2 will report a file checksum error while downloading even if its correct.
Do you have public URI link to reproduce this?