1- basing your offense around an awesome, but occasionally reckless QB that will do anything for a first down. Then not having prepared supporting backups in place to step in if the inevitable were to happen.
2- training and encouraging the defense to be so aggressive that concussions, broken arms, twisted ankles and other such injuries become a product of the system. Not to mention the multitude of mind boggling personal fouls and late hit penaltys that are a result of the emphasis placed on big, hard, aggressive hits.

In addition, running a high tempo offense that is attributing to the physical deterioration of the players.

I've been a Coach Mendenhall fan since he was hired from New Mexico, but I'm starting to question many of the things he has preached and designed his program around.
In my opinion, as of the Nevada game he has lost the teams and as of the Boise St game he has lost the fans.
I don't see him bouncing back from this, due to what he has built the program around 'on the field'.