Here is what we know:
Start of the season
Kyler openly disliked Kliff's play calling. Kliff tried to teach him a lesson in the preseason by having him call plays and the offense worked better with Kyler calling the plays.
Mid Season
Kyler was not given freedom to change plays to the level he would like. It culminated with someone asking why a certain play was run and he said "I am running the plays I am asked to"
Right before Injury
Schematically (bleeped)
So yeah I absolutely believe that Kyler was overtly frustrated with Kliff and that negativity was seeping through. I also think it's an issue that he can't rise above it all. Whomever is the next coach needs to be able to teach this kid how to man up.