Plot hole: Beckett and Castle lose their cell phones and wallets and are being chased by the mob. Beckett steals a cell phone from a car but can't use it, since it is locked and then shut off remotely. Any cell phone can always dial 911, whether locked or blocked from service.
Continuity mistake: After Beckett gets back from her assassination assignment, she washes up in a bathroom and places the gun she was given in her front waistband near her stomach. Then she goes to meet Lazarus (Vulcan Simmons) in the basement, who realizes she's Beckett. When she pulls out the gun, she reaches behind her back to get it.
Continuity mistake: In the flashback of Beckett and Montgomery, when Montgomery finds her in the archive room studying her mother's murder case, Beckett says that she was unable to find any leads worth following. But in season three, when Montgomery explains to Castle that that encounter was when he first met Kate, he says "she found some things that didn't add up", suggesting that she did find a clue worth investigating.
Continuity mistake: Beckett's sweatshirt changes position on her left shoulder throughout the scene in which she and Castle are sitting in bed discussing Bigfoot. Her sweatshirt is initially covering her shoulder and then keeps going lower and lower off her shoulder every time the camera comes back to her .
Factual error: The team is discussing the location of the Widmark hotel which the detective says is downtown. Beckett then looks at the map and locates it only 5 blocks from E 72nd street, which is UPTOWN in NYC. Furthermore the map shows E 72 intersecting Broadway which is on the west side of Manhattan. This entire mapping exercise is incorrect.
Other mistake: The security camera images of Castle kissing Kyra on the roof are completely inexplicable. The angle at which the images are taken are near enough identical to the angles at which the rooftop scene were shot. There were no pillars, poles or high walls for a security camera to be attached to at those particular angles, so where did the images come from?