Continuity mistake: After Special Agent Shaw tells Beckett to go home when they believe a murder took place in a multi-story car park, Beckett touches her hair with her right hand. She is wearing gloves on both of her hands when she does this. In the shot immediately afterwards however, her right hand is bare and she is holding the glove in her left hand.
Continuity mistake: When Castle gets back from helping Alexis with her friend and thanks Beckett for taking care of Fagan (Alexis' egg), just after her line, "Yeah well, he was easy. He didn't even fuss when I put him to bed", Ryan and Esposito come in and Ryan is holding a missing persons poster of Elizabeth McGinty. As soon as they walk in, Ryan is holding the poster with the front facing the camera. But two shots later he is holding it with the back facing the camera.
Continuity mistake: When Beckett goes to the bathroom to read Castle's book and Castle peers over the top of the cubical to tell her what page the sex scene is on, she is holding the book with her fingers between the pages dividing the book into 2 sections. These 2 sections switch to 3 and then back to 2 between shots.
Continuity mistake: When Beckett, Castle and Capt. Montgomery are walking through the precinct, after Castle and Beckett checked on Alexis as she had been categorizing personal belongings, and Castle is talking about how he watched Alexis from the bushes the first day of preschool; Montgomery states he followed his son's bus all the way to the Adirondacks. In the final episode of season 3, Montgomery had his two daughters, and wife at his funeral. There was no son.
Continuity mistake: In episode 2-5, "When the Bough Breaks," when Rick is talking to his mother regarding handing out her pamphlets at his book signing party, he opens his beer and throws the cap on the counter, when the shot changes you see him opening the beer again.