Continuity mistake: S02E06 - Black Gold and Red Blood. Lisbon comes to visit Jane in prison. She brings him a muffin in a white paper bag. In shots facing Jane, the bag faces outward. In shots facing Lisbon, the bag faces towards the middle of the table.
Other mistake: When Jane is setting up for his escape from prison, he captures a wild mouse. Then he presumably holds her in his hand for the whole time. I've handled mice, and when they're scared, they bite hard enough to take chunks out. There's no way a wild mouse would stay in human's fist that long without drawing blood.