I never heard for sure, but I think it is because they didn't let the clock run out and made Auburn come out and run 1 more play. The rules dictate that the clock stops on change of possession, and it was 4th down. However with a few seconds left in a 49-0 game they could have dragged their feet a little.
Auburn wanted that play to get their rusher to 1000 yards. Saban was probably mad because they got it.