Leaf had a poor relationship with his teammates, whom he tended to blame for his poor play, and with the media. In one embarrassing locker room incident during Leaf's rookie year, he was caught on camera screaming at a reporter ("Don't...talk to me alright! Knock it off!" Leaf said) and had to be physically restrained by teammate Junior Seau. Another on-camera incident involved Leaf confronting a heckling Charger fan during a practice session. Two coaches had to restrain Leaf and escort him off the field. Leaf had a particularly bad relationship with former Chargers safety Rodney Harrison, who described being a member of the Chargers during Leaf's rookie season as "a nightmare you can't even imagine." After hearing that Leaf retired in 2002, Harrison was quoted as saying, "he probably did the best thing; he took his money and ran."

The quarterback missed all of his second season in 1999 when a shoulder injury was discovered during a pre-season physical. He was put on injured reserve but continued to make headlines for, among other things, getting into a heated shouting match with the Chargers' general manager Bobby Beathard and another coach. That incident resulted in a fine and a suspension without pay. Leaf also allegedly lied about a hand injury in order to get out of practice so that he could play golf instead and for playing flag football despite his injury