9 wins is really good. That said, ARod's issues these last three weeks:
1) Eating up the clock while playing from behind. This plan may be because of injuries on the defense, less confidence in the the offense to move the ball consistently or something else. I'm guessing this is discussed staff-wide. BYU's offense statistically scores more when they run plays in under 19 seconds. And it isn't close. Change up the tempo from time to time. Keep the opponent's defense guessing.
2) It seems that he sometimes gets too cute with his play calls when the team is rolling. The best example was the fade call against KU. The team had three straight runs – making nearly 10 yards per attempt. Just run it into the end zone. This may have been another staff decision to eat clock (although an incomplete pass would have just stopped the clock). Focus on scoring more than eating the clock (see #1).
3) QB recruiting. Retzlaff is an above average QB. He's vastly improved since last year. His INTs to end the half against KU and to end the game against ASU were devastating. It seems that ARod's offense needs a running QB. Retzlaff is probably injured because he hasn't run well the past 3+ games. It seems that the QB room should have someone that can step in and help when he's struggling. I don't know the QB room, so I'm guessing that BYU is playing the player that gives them the best chance.
NOTE: I hear from people that know football that ARod's system is good. The issue is often the execution by the QB, missed blocks by RBs (or lineman) or WRs not making plays. As BYU gets better players, much of these issues may be cleaned up.