I watched the aTm-Neb game on DVR. Here's my opinion of the refs in that game.
Calls against Neb:
2 false starts - both legit, 1 was just a hair early
2 illegal formations (1 declined) - both legit, WRs not on the line
2 personal foul on kickoff returns - not on camera either time
1 personal foul on Cotton after he fell on fumble - it sucked because he was getting abused and the ref missed it - but they often only see the retaliation
1 unsportsmanlike on Cotton right after that - it's hard to believe he said something worth another 15 yards, he was just standing there apparently trying to tell the ref that his nuts were getting jabbed and grabbbed
2 off holding - both legit, one grabbed and twisted his man, the other was falling backwards and pulled his man down
2 def pass interference - 1 was blatant on Nebraska, the other should have been offensive PI on aTm, as mentioned by Herbie
1 unsportsmanlike on Pelini - after the personal foul on a kick in to the end zone - he was ranting quite a bit, so he probably earned it
1 roughing the passer on 3rd and 11 near midfield with about 6 minutes left in a tie game - Absolutely horseshit call that kept alive aTm's possession for the final FG of the game
1 - intentional grounding on Martinez - he could have been called down or stopped already, but there's no markoff for grounding, so either way the ball ends up where he was
Other calls/non-calls of note:
Interception by aTm on the sideline - it was ruiled inbounds, and the replay was inconclusive whether his left foot was down inbounds before the right foot was on the line, so replay understandably let the call stay
1 minute left in the first half - clear hold on aTm was missed
Once Neb was granted a timeout just before the play clock expired, avoiding a delay penalty
3rd and 7 on Nebraska's drive when they were down 3-6: def pass interference was called, then they waved the flag off, making Nebraska kick the FG to tie raather than having a 1st down in the red zone. The call was a touchy one, and a no call wouldn't have raised any eyebrows, but why throw the flag and then decide afterwards it wasn't a penalty? The ball wasn't tipped or anything.
Overall, it was about as frustrating as the calls in the Iowa-tOSU game. Almost all of the holding and PI calls/non-calls went the home team's way in both games.
The 'late hit' on the QB was a terrible call on a perfectly fine hit to the QB right after he released the ball. It led to the game-winning points, which made it even worse.
The 2 calls on Cotton were sheer incompetence in breaking up the pile and seeing what was happening, but when the ref saw the kick he had to call it. Adding another 15 yarder for complaining seemed unnecessary.
So it was a poorly officiated game, and the home team got the vast majority of the calls, but that happens fairly frequently. As far as suspicions of the refs wanting to influence the outcome, it wasn't as bad as some things I've seen in the SEC the past couple of years, and it wasn't close to the 2007 Pitt-WVU game.
I'd only consider 3 things egregious: The double-penalties on Cotton, who was the victim, one PI that should have been offensive PI on aTm, and the pathetic roughing the passer call with about 6 minutes left.
That's above average even for Freek. Love the Husker player with a corn cob in his back.