Just expanding --
The Onside Kick Game, Oklahoma at Oregon 2006 and The Fifth Down Game from 1990 have to be the two biggest screw-jobs in recent history of college football. They have these things in common:
1. Relatively high-profile teams. Colorado was ranked #12 at the time of their game, and Oklahoma and Oregon have both been highly-regarded programs the last few years.
2. It determined the outcome of the game. The mistakes by the referee crews in these games literally, inarguably caused one team to lose the game. It's a somewhat frequent occurrence for bad refereeing to contribute to the outcome of a game, but something else entirely more rare to be the single determining factor of a game's outcome.
3. They were not "close" calls. Nothing like pass interference, or a push-off, or possible possession. They were basic rules of football that were flat-out ignored, single-handedly determining the outcome of a game.