ND played an FBS team, not ND's fault they're not a good FBS team.
An easy way to fix this is don't count FBS team games against non-FBS competition. Go ahead and schedule a scrimmage if you must, it's just not going to count towards your win or loss total.
Indiana would be screwed. Third straight year they've scheduled 3 non-FBS teams to open their season. Such competitors.