ND owned them in the field position battle as well. That may have played into ND having fewer yards - they had a shorter field to run, while Michigan generally started all the way back on their end.
That said, they seemed discombobulated as a team. Sort of like the damage that has been done can't be repaired - much like how I see Texas this year. They'll fight, but they don't have the confidence that a big-time program should have. The players know the fans and media are talking about them, and discussing whether Hoke will make it through the end of the season. It can't be good for the players' psyche.