Handling of integrity errors when declaring files is insufficient
If there is an integrity error when declaring a file the whole process is retried once. But if there are multiple files being handled simultaneously which all contain several identical, new, parameter values or runs (or similar), this might not be enough.
The brute force solution would be to retry multiple times (but it shouldn't be forever, because a database inconsistency could cause the server to get stuck).
A more elegant solution would be to put the transaction into serializable mode, then retry any serialization failures until success. But this has other implications that would need to be checked.