I would suggest having the TA (if it's a person, not an OTA) call AC to correct. They will be in the best position to explain what happened and verify the second payment to QF. Otherwise, you could be proactive and call the SE reservations,but I am not certain that would work, given they often will not touch a booking not made by AC. Or, as you suggested, wait and see what posts and then file the on-line form for any discrepancy.

Best of luck! This seems like it may take some work to get resolved.