Well, you raise an interesting question. Goodell claims that he was not made aware of the Colts' complaints prior to the AFCCG. However, the Colts claim they informed someone at the NFL office prior to the game.
So the question is a matter of how responsible he is for the actions of those that work for him. Either he is lying, in which case he should have his feet held to the fire, or he is telling the truth, in which case he should have his feet held to the fire. However, if he is telling the truth, I cannot imagine he is terribly happy that someone who works for him in the league office got a call from the Colts about this issue prior to the game and did not bother to pass that info up the chain of command.