Continuity mistake: A man attacks the judge by running out of the shower. When he runs through the shower, a shower curtain is draped over him. For most of the scene it is over his head, but when he is dragging the judge into the shower, the curtain has moved off of his head and is even gone completely in one shot, perhaps to make the actor more visible.
Continuity mistake: Just before Shawn notices the abrasion on the corpse's scalp, the two men put the man's arm in the body bag and begin to zip it up. They then put the same arm in the body bag again, as the stain on the man's shirt front is shown.
Visible crew/equipment: S01E13 - "Game, Set. Murder?". When Shawn and Gus runs out of the crime scene apartment, heading for the restaurant across the street, you can see the camera and a crew member sitting on a chair reflected in the mirror behind Gus.
Continuity mistake: When they are talking to the two kids outside of the school for the first time, one of the kids has a juice box. Shawn starts talking and it shows from behind the one kid with the juice box and he is about to take a sip, then the shot changes and the juice box is by his side.
Continuity mistake: In the restaurant, Byrd slamms Tancana's face into a burger and mustard/ketchup smears across the left side of his face and nose. In the echo, the condiments are on the opposite side of his face. After Tancan drops down behind the seat and then reappears, most of the condiments have been removed, but the glob on the left side of his nose is lower and more on the top of his nose than it had been before. (Not a change that would have happened from him rubbing it off and missing some.) The blob continues to migrate throughout the rest of the time they are in the car.
Plot hole: The flashback involves Young Shawn and Gus getting ready to go to a comic book convention, Shawn in costume, with his father's consent. This contradicts the flashback in "Shawn Vs The Red Phantom," where Henry won't allow Young Shawn to even read comic books or play superhero with a towel around his neck.
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Continuity mistake: In the scene where Shawn is brought into his childhood bedroom to investigate Allison's abduction, there is a "Peeping Tom" band poster visible behind him for a few seconds. This was Shawn's bedroom in the 90's, and "Peeping Tom" didn't exist until 2006.
Continuity mistake: When Shawn calls the first student up to the board to write a number, firstly the written number is 6.00214, which is an incorrect Avagadro's number, but it is not always this incorrect number. At some point during filming somebody changed it to the correct number: 6.02214, and you can see the number actually changing back and forth between the two numerous times during this scene.