Unfortunately that wasn't it. I've never changed my auto-subs level and after he failed to appear for a bunch of plays in a row, I actually lowered both the sub in and sub out level for my entire defense. He stayed out the rest of the game.
That's pretty sloppy on EA's part, if true. You should always be able to see who isn't in the game and why. This guy is my best defender and he was out an entire quarter.