Yep. The "muffed" punt call looked bad at full speed, but technically it was right according to the rule. The only one I've seen that I might disagree with is the "bobbled" catch on third down back during ND's first drive, which at this point is fairly moot given how ND's playing overall.
Actually there is no rule in college about giving any sort of buffer, but the rule is you can't interfere with the catch. The Alabama returner didn't call for a fair catch until the last second and the Notre Dame player didn't touch him. In fact in college football if your own player is blocking into you and you muff the punt, it isn't a penalty. It was a bad call and an incorrect call.
In addition the catch was also a bad call. If you come down in bounds with clear possession then you simply have to not lose possession during the follow through, the player came down with clear control and possession and never lost possession, therefore it counts as a catch.
I watched exactly 4 minutes of this game, the first 4. After those two egregiously bad and 100% incorrect calls, I stopped watching as I won't watch a game that the refs have already decided that Bama was going to win. College football has officially lost me for the remainder of the BCS era at least.