I completely agree, there were a few good calls but there were several that took away scoring opportunities away from Nebraska.
One thing important to remember, and this isn't directed at you but just a thought on my part, is that Nebraska realized that Colorado could not score on Nebraska's defense, or at least not enough to get back into the game in the second half. Colorado began to load the box on defense, knowing Nebraska was going to run the ball. And Nebraska did with so-so success, with a lot of plays negated by penalties - some that were deserved but many that were not.
Nebraska decided not to throw downfield against Colorado despite them loading the box simply because that was a way to win the football game. The only possible way Colorado could get back into the game was via a pick-6 or other turnovers. So Nebraska ran the ball, worked the clock, and punted. I think if they really wanted to, Nebraska's offense in the second half probably could've produced another touchdown or two. But they opted for complimentary football when they were up big.