This thread raises further the issues of how airlines actually credit to FFPs. And in some retroactive claims I've had the same response as OP that the airline has credited to one FFP that they shouldn't have.

Interestingly I had once a UL flight where by default my travel agent had put my CX MPC number to it. At the airport I requested to change to BA and BA was correctly reflected in my BP. But when I completed my trip, I noticed the miles were credited to BOTH CX and BA. Strange indeed...