The SEC sent out an email explaining the decision to allow Auburn to kick a field goal at the end of the first half on Saturday. From aldotcom:
At the end of the 1st half in the Alabama vs Auburn game, during a play that resulted in a first down inbounds, the game clock went to 0:00. Replay stopped the game to review the clock. The decision from the Instant Replay Official was that video evidence showed there was 1 second on the clock when the player was down so the clock operator was instructed to put 1 second back on the game clock.