All of the above.
He had a lot of work ethic/fitness issues, including chain smoking, eating habits, staying out late, etc.
This wouldn't have been a big deal, save for the fact that he was getting hurt all the time and complaining of having a bad back. There was the perception he was dogging it and it didn't sit right with certain guys who were watching Larmer and Graves go out there and battle with bad backs, or Leetch having to pick up even more slack and run himself into the ground.
There was tension with the coaching staff, the training staff, teammates, etc. The boiling point came when Steve Larmer threatened to knock him on his ass during a practice if he didn't get his shit together.
Contrary to popular belief, the most damning internal relationship to impact Zubov was not Messier. It was Leetch, Lowe and Larmer.