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.
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?
Character mistake: In the scene where Castle and Kate are being told that the victim's SIM card is broken and the last two digits of the phone number are missing, Castle says that they have 99 possibilities, which mathematically is wrong. Obviously the writer didn't count the combination 00. The correct number of possibilities is 100.
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.