Character mistake: When Kim is trying to convince Lisbon to help the FBI on their case, she says Jane stopped the ten-year reign of a mass murderer. Red John was a serial killer, which, by the FBI's definition, is a criminal behavior distinctly different from mass murder; he may have had a large number of victims, but he killed them either one or a couple at a time, with a cooling-off period in between, not all at once.
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Deliberate mistake: When the investigators are in the basement wine cellar, they turn on their flashlights to illuminate the pitch black area as they walk around. However there is a light source moving with the camera shining on them as they are casting a shadow behind them.
Continuity mistake: Lisbon and Jane enter the interrogation room to interview the wife of the murder victim. As Lisbon sits down she opens her notepad upside down. Next shot of her the notepad is right side up. Remaining shots of Lisbon shows the notepad upside down again.
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.
Continuity mistake: When Jane speaks to the owners of the restaurant, the female owner is writing something and also has a drink. She takes the drink with the pen in the same hand. When the shots changes, the pen is no longer in her hand. The shot goes back to the original position and the pen appears again.
Character mistake: Towards the end of the episode Patrick Jane plays a game of chess with himself. He moves the queen and states check mate. It is not checkmate, black knight would take the queen in the next move. It is in fact a flawed example of scholar's mate, something that someone of his supposed intellect and chess skills would not be rehearsing.
Continuity mistake: In the beginning when Patrick is talking to the widow Erica Flynn at the police station, when she first leaves the interrogation room the zipper in the back of her dress is down about four inches. As she is walking to the elevator, when she goes into the elevator and turns, you see that it is now zipped up completely.
Continuity mistake: This happens right at the very end at the hotel room in Mexico. Jane and Lisbon are sitting on the bed and the cellphone rings. It's Red John calling. There's a beer bottle next to the phone on a round table. At first the label faces towards the middle of the table. When Jane picks the phone up, the label now faces the other way.