Revealing mistake: Any time any character is driving a Suburban, or any other vehicle with a column mounted shift lever, the shifter is in park while they appear to be driving.
Strawberries and Cream: Part 1 - S3-E23
Plot hole: In the heat of killing fake Red John, Jane forgot to notice that Craig O'Laughlin never knew about the mall setup to lure Red John. So definitely Gale Bertram himself was in contact with the serial killer which he may have missed first up, but all that time in jail afterwards he could have figured it out.
Strawberries and Cream: Part 2 - S3-E24
Continuity mistake: In S03E10 Patrick Jane obtains Laroche's suspect list "through back channels" from Virgil Minelli. In this episode Patrick Jane obtains Laroche's suspect list again, through bluffing with what Laroche is hiding in his safe.
Orange Blossom Ice Cream - S7-E3
Continuity mistake: In the meeting they said Erica Fline broke out of jail a year ago, but that occurred three years previously. (00:01:53)
Green Thumb - S6-E10
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.
Factual error: Any time FBI agents enter Mexico, they are always armed. Mexican law prohibits U.S. Agents from bringing weapons into Mexico.
Factual error: Lisbon is sending Van Pelt to El Oro State Forest. Van Pelt says, "El Oro State Forest, that's east of Lake Tahoe, right?" Lisbon says, "Yeah." East of Lake Tahoe is Nevada, not California. (00:01:17)
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.
Other mistake: Carrie the assistant brings Lisbon and Jane to Stutzer's office. She swipes her card to open the door. However, she does this upside down, swiping the bar-code instead of the black magnetic strip, on which she is holding. (00:09:30)
Red-Handed - S1-E6
Continuity mistake: After Lisbon gives Patrick the $100 he is seen walking to the table handling chips. But when he sits down, only then does he convert the notes to chips.
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.
Factual error: The container for the dangerous biological material is marked "Biohazard Level 5." There is no level 5. According to CDC regulations Biohazardous materials are rated 1 through 4. Based on the description of the material in the episode, it would be required to be stored in a laboratory rated at Biosafety Level (BSL) 4. All BSL 4 labs require personnel to wear a fully enclosed, pressurized suit when inside the lab. (00:01:05)
So Long, and Thanks for All the Red Snapper - S4-E22
Continuity mistake: Cho opens the vent with a screwdriver and hands it back to the landlord (who pockets it). In the next shot Cho has it in his hand again finding the hidden drugs. (00:10:00)
Continuity mistake: Patrick Jane takes a sip of water just as he is about to propose to Lisbon. The way he holds the water bottle changes.
Days of Wine and Roses - S5-E11
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.
Black Gold and Red Blood - S2-E6
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.
Red Menace - S2-E4
Continuity mistake: S02E04 - Red Menace. Jane is teaching the victim's son how to drive. His seat belt is alternatively fastened and unfastened.
Black Gold and Red Blood - S2-E6
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. (00:31:50 - 00:33:10)
Every Rose Has Its Thorn - S3-E19
Continuity mistake: In the scene where Agent Lisbon is asking Jane why he's obsessed with the woman he's investigating, Lisbon's pen is in her right hand. But when she waves, the pen has disappeared, but in the next shot it's back in her hand.
Red Hair and Silver Tape - S1-E2
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. (00:09:35)