He would go in at 2am, 4am, etc and put up hundreds of shots. They changed the locks. He would wedge open service doors, etc. Risk was burnout or injury from sheer repetition.
They might've underestimated the sort of character he is. There are some great stories out there about his training habits, the Lakers scouting him as a rookie pre-draft, etc. Contentious character, but hard to deny his focus.
There is one great story of him calling in a trainer to work with him after midnight. They take a break, the trainer understanding they were done for now and going home. Trainer came back in the morning for team training and made smalltalk with Kobe about hopefully he had had a good rest after their workout. Kobe was confused. He'd been there all night training and hadn't gone home.
Because of injury or potential for injury. The team wants Kobe Bryant healthy and on the court, so wants to limit excessive practice to avoid reinjury or new injury.