One issue I had was when Geno Stone cramped up in the back of the end zone on our last field goal drive. He gets treatment from the trainers and comes off as required for one play. Iowa State calls a timeout to figure out what they want to run, and he comes back on without us running a play.
This is not allowed, which honestly I didn't know until Oregon vs. Auburn this year when Herbert got hurt, Oregon called a timeout before their next snap, and Herbert tried to come back but the refs wouldn't let him because they hadn't run a play yet. That is something that every ref should know, and it is not a bang-bang play, you just have to be paying attention. I don't think it would have made much of a difference, but it does show the general incompetence of some refs.