Character mistake: When Neal tells Rebecca about an Indian Idol and describes the idol to her, she tells him it's the Hindu Idol of Seeta, the goddess of wealth. Actually the idol is of Goddess Laxmi.
Continuity mistake: At the end of the episode, the Mercedes S class that is burning is not the same car that Castle drove previously in the episode, it's an older model one. Either it's a mistake or has to do something with the plot resolution, decide yourselves...
Visible crew/equipment: At about 30 minutes into the episode, right after Cal says: "if Jeffrey knows about priox, he's going to jail. But I'm gonna be damn sure before I send him there", you can see a hand in the top right corner of the screen.
Visible crew/equipment: At the end of the episode, when Alicia is listening to the audio recording on her laptop in bed, you can see the hand of a crewmember on the corner of the white cupboard at the left side of the screen. (00:42:45)
Visible crew/equipment: In the rec hall, when Kensi feigns sickness while posing as a cadet the gunman jumps off the stage, and as Kensi bends over the small rectangular bulge of her mic pack can be seen at her back. (00:30:25)
Continuity mistake: When Pete and Myka first get to Warehouse 13 and walk up, the football that flew at Pete is lying on the ground close to the open door. In the overhead shot, the ball is gone, but is there again in the next closeup.
Episode #3.1 - S3-E1
Continuity mistake: DI Chandler calls a suspect "Daniel Wilkie." However when the interview is done he goes and talks to Ed, saying "you've just arrested Ben Wilkie."
Factual error: At the beginning of the episode, Patrick Swayze is looking at photos of two Iraq veterans who have been murdered. He identifies one as a Marine Lance Corporal and the other as an Army PFC, but both pictures show men in U.S. Army uniforms. A bit later, his partner, who is supposed to be a Marine vet, refers to his decision not to "re-up," using the Army term for re-enlistment, rather than "ship over," as it's referred to in the Navy and Marines.