I'll just go ahead and address the preparedness side of things - he dropped a lot of weight after the injury and never put it back on. This was public knowledge as Harbaugh even said it. However, he didn't handle Harbaugh calling him out well. He was late to meetings, games, and apparently racked up an impressive fine tab.
There's one more incident that I know of that apparently really pissed coaches off, but I don't feel it's my place to publicize that. Feel free to PM if you'd like.
that does make a lot of sense tbh - just really disappointing because he's so talented - was one of my favourite players ever to watch on tape to and evaluate