Actually, I noticed a couple calls, but I think the fact that they didn't really mean anything might be why the complaints are very few. The first one I thought was bad was the long pass to Toomer early in the game. There was a ref right behind the play and it was a pretty obvious offensive PI on the replay. He shoved the CB back with a hand to the face to create separation. Eli threw an INT a couple plays later so it didn't matter.
The other one, which was awful was the measurements with about a minute and a half left. They basically gave the Giants 2 two timeouts. I also still don't get why they put time back on the clock to 1:28. Then on the play after that I hit rewind and counted from when the whistle blew to start the clock (clock didn't run) to when Manning got tackled and it was a way more than 8 seconds. Coughlin came out onto the field well after Eli recovered his own fumble to call the timeout. I still don't get how in the world that one play took only 8 seconds. You can run off 8 seconds on an imcomplete pass, let alone a QB dropping back, scrambling out and getting tackled. That said, the Giants still had more than enough time to score, but in this case without the play stoppage and free timeouts, it is conceivable that they would have had to spike the ball and the play calls might have been different.
I think there was some other minor calls, but for the most part I think they did a good job and the major misses probably didn't affect the outcome.