issue:

BYU had 3 penalties on 3rd down.

Here were all third downs with the yards to go:
3rd & 2 (incomplete pass)
3rd & 10 (5 yard pass, converted on 4th)
3rd & 7 (incomplete pass)
[Then there was a 74-yard touchdown drive with no 3rd downs]
3rd & 4 (incomplete pass)
3rd & 3 (false start)
3rd & 8 (incomplete pass - field goal on 4th)
3rd & 4 (complete for 11 yards)
3rd & 2 (TD nullified by holding penalty)
3rd & 12 (incomplete pass - field goal on 4th)
3rd & 10 (9 yard pass)
[Then there was a 77-yard touchdown drive with no 3rd downs]
3rd & 5 (40 yard QB run nullified by 2 holding penalties)
3rd & 15 (12 yard rush)
3rd & 1 (rush for no gain - final kneel down on 4th down)

So in addition, all of the penalties were on 3rd downs with 5 or fewer yards to go.

Fix the penalties, solidify the run game to shorten the third downs, and I think you'll see some improvement.

I don't think it's a play-calling issue. Just bad circumstances, due to penalties and injuries to BYU's top 3 running backs.

They'll be fine.