When the guys are shooting the basketball, the ball is a normal basketball. When Danny tells Jesse that Comet could shoot better than he can, the ball is switched to a different type of ball. You can tell it's different because it's a shiny ball. After Comet shoots the basket, the ball goes back to a normal basketball.
When Comet makes the basket, it is obvious he is not played by the same dog as usual, as the hair on his face is noticeably darker.
When Jesse tells the family to leave the court and let him try and figure everything out himself. When he's supposedly alone shooting around, he shoots an air ball and a hand appears quickly, catches and throws the basketball back to him.
Jesse mentions that he has always hated sports. But in seasons one, he is interested in football and basketball, and is DJ's soccer coach in season two.