To add a bit more details to that WARN message - It appears that when a subordinate tx is imported as follows (that 300 value is a example timeout):
final Transaction newSubOrdinateTx = SubordinationManager.getTransactionImporter().importTransaction(xidTransactionID.getXid(), 300);
it ultimately leads to com.arjuna.ats.internal.jta.transaction.arjunacore.subordinate.SubordinateAtomicAction constructor which adds it to the TransactionReaper. But I don't see any code which removes it from the reaper once the SubordinateTransaction is committed/rolledback well before the timeout. As a result, the TransactionReaper ends up logging that WARN. So I'm not sure whether it's just a case of removing the ReaperElement from the TransactionReaper or something more. Let us know if you need more details.