1. I don't know why, but Kansas looked like they traveled with a very small team, there weren't a lot of players on the side line. I hadn't seen that few players since the first game of the season with SIU. Because of that BYU should have played at tempo (I didn't say up tempo) to gas KS by the second half, which would have been one of BYU's advantages for the game. This would have made BYU's offense more dominate in the second half.
2. BYU's slow play allowed KS defense to get breathers while in the game. This is actually a pretty big deal if you can get almost a 40 second breather between each play. It was pretty frustrating to see the ref set the ball, BYU get the play call, then send in a sub with 25 seconds left on the play clock, then see BYU huddle again, to break huddle with 10 seconds left. That gives the offense no time to look at the defense to figure out potential receiver routes or adjustments, blocking assignments etc. They also didn't do any motion pre snap, other than Martin and what the heck was that? Send him out, run him back and past and then run back for the handoff? The guy was running 35 yards before he even got the ball.
3. BYU's offense was doing exactly what the previous DC philosophy was trying to accomplish, the bend don't break rule. The defense wanted the other team's offense to make long extended drives because they expected the offense will make a mistake and therefore blow their own drive up instead of any defensive pressure. This is exactly what BYU's offense did, they made the mistakes and it wasn't because of any spectacular play by KS defense.
4. This is the biggest one, the offense acted like they were not interested in playing, there was no excitement on that side of the ball, no sense of urgency, no sense of attacking mentality, just a feeling of let's just go through the routine. No killer instinct. Chase Roberts said it in his post game interview, they need to run the offense and get up by 20-30 points so they don't need to rely on a last min drive.
There are other things, but these are the ones I will mention.