I've had it happen. I had a loaded 9mm Beretta mag in my laptop case. I think I was flying home from the Memphis airport. I had been all over the hotel room and rental car, and finally just figured I must have have only brought the 2 mags.
Mag 3 fell out on the floor as I was unloading the laptops out in the gray bins at security. I showed it to the TSA guy and he just advised me to tape up the ammunition in the mag and check the bag.