New HC with a new offense and a new defense. That's a lot for any team to take in and adjust to. Combine that with the fact that 3 of BYU's starters are new to the team - and 2 of those are freshmen new to the college game.
I think we should expect it to take some time before the team performs to the degree that we're hoping for - they need to become more and more familiar with it until they don't have to think about what they're doing, they just do it.
I think that 2-3 years down the road we'll see much improvement as there will be a core of returning player who understand the offense and there will only be 4-5 new guys coming to the team who are learning it for the first time. Right now, it takes all 5 guys on the court remembering the new schemes and plays - I'd be surprised if there aren't multiple guys out of place at times. That should happen less and less frequently as the players get more used to the schemes and then you combine that with consistency among the coaches (or at least among the schemes) and returning players from year to year.