[PvK]

A guess:

Maybe the player accidentally ran the same turn twice in a row (OR, he accidentally sent the same orders file twice in a row), and so the orders file he submitted (for the turn before you noticed the problem) was for the previous turn, and therefore didn't work. Meanwhile, the game server saw this as a couple of bad turn submissions from that player, and so had the AI run his empire for him in the meantime.