The only time he'd make exceptions would be for "his" establishment players that he felt loyal towards.
We could easily look at the situation in 2010-2014 (not giving Hendrix even a shred of a chance, etc), but 2015 and 2016 were two of the more notable years where his choices could easily be questioned.
It's no secret that Joe Schmidt was all but crippled after that cheap chop block by Navy in 2014. Before that injury, he ran about a 4.85 on a good day. After that injury, there was no way he would run any faster than the 5.1 mark during that 2015 season.
While he was a very smart fellow on the field, and did a decent job of calling defensive audibles, not being able to keep up with even the slowest of tight ends showed a terrible weakness in the defense, and of all times, this terrible mistake couldn't be pinned on Brian Van Gorder. In all honesty, that was a veteran defense, full of NFL talent, and they were smart enough to adjust on their own without the audibles. How many times did we give up a very easy pass over the middle because Schmidt couldn't cover? How many times did a running back juke him with a very simple cut move?
2016 was where he kept playing Malik Zaire at the QB position, out of loyalty for his work in 2014, even though he kept stinking up the field. There was absolutely no question that Deshone Kizer was the best QB on the roster, yet Brian Kelly kept giving Zaire too many opportunities, which killed many a promising drive. That loss to Texas should never have occurred, since we were scoring every time Kizer led the team, and stalled out every time Zaire led the team.