Claeys was asked about it yesterday on KFAN's weekly show. He said the big ten doesn't have to say much in their response. I don't know if that's actually true or if Claeys just didn't want to get into it. He did say that every call that is sent in is then sent to every official in the big ten with an explanation as to why the call was right or wrong. So at least every big ten official got to see the plays from last weekend and are aware we got screwed. As far as discipline, who knows.
It happens from time to time but it is pretty rare when the conference comes out and makes any sort of public statement about a call that may or may not have been missed in a game. As jaymil laid out it all takes place behind the scenes, and is handled out of the public eye as well. As to the point of not publishing the names of refs and what there is an obvious reason for that and that is the crazy fans that send out death threats and other nasty messages any time there is a bad call in a game.
I am not going to sit here and pretend the refs do a great job all the time, we see missed calls every game but it is way harder than fans ever give them credit for. Refs don't have the advantage of seeing every play from multiple angles, they get to see it one time, live, moving at a 100 miles an hour with lots of other stuff going on at the same time. Refs can get it right 99 out of 100 times but all anyone ever talks about or hears about is the 1 blown call.
I had the good fortune to get to know a Big Ten ref, he has since moved on to a different conference but during the time he lived out here we spent a lot of time talking about how they do things. The refs watch film of every call they make as a group after the game. They review all their calls and grade themselves on if it was a good call or a bad call. The Big Ten office then also reviews every call that was made and grades it. The grades determine what assignments the refs get in future games as well as bowl games and what not. Enough bad grades and you don't have a job next year.
The one point he made to me is that as a group these guys take their job very seriously and the last thing any of them wants is to be the reason a team wins or loses a game on a blown call. He was personally haunted by some of the calls he had missed over the years and said it was really amazing the difference in perspective you get seeing the call from above on video as compared to down on the field live.
As for calls that get sent in by coaches they are all reviewed by the league office and the league refs. There won't be a public statement but it is communicated if a mistake was made, make enough mistakes and you lose your job. The thing that bugged him the most was this idea that the refs are instructed on how to call the game in order to favor one team over another, it just isn't true.
Fans are always going to complain about the officials and they are always going to think the refs are out to get there favorite team. It is a shame that more people don't grasp just how hard this job is or understand just how seriously the people that do it take it.