Continuity mistake: On the train, the man who approaches Reese wears a silver necklace, which jumps in and out of his top throughout the scene. (00:01:00)
Continuity mistake: A man tries to take Reese's bottle, only to be startled when the seemingly asleep Reese grabs his hand. Throughout the scene, Reese's scarf is either in his hand or not. (00:01:05)
Continuity mistake: While Reese and the witness are hiding in an apartment, the door is opened by the student to dismiss the bad guys with the chain lock on the door. The door is open about 18 inches and yet when the student closes the door the chain lock is normally sized about 4 inches and is still attached.
Visible crew/equipment: There is lighting equipment reflected on Carter's sunglasses when she confronts the FBI agent who is following her. (00:26:45)
Root Cause - S1-E13
Factual error: Finch's trojan tracker displays "accessing network on IP 623.173.93 .225.9." Not only is 623 an impossible number for an IP address to have, as they only go up to 255, it's also made up of 5 parts, instead of the 4 which IP addresses are limited to.
Visible crew/equipment: When Reese and Saunders are nearly crashed into at the construction site, as Reese is exiting the vehicle you can see the stunt driver is the one sitting in the driver's seat instead of Saunders. (00:18:45)
Continuity mistake: Mr. Reese and the stockbroker are hiding out with the street people. In the portion of the show entitled "Kill Squad," at about the 2:02 mark, Mr. Reese is building a fire in a steel drum. The paper and wood are nearly overflowing as he continues to prepare the fire. They cut to Mr. Reese spraying lighter fluid onto the pile of wood and paper. However when Mr. Reese throws in the match to ignite the fire, all the debris are way down in the steel drum. As the flames come upward there are no signs of the wood or paper that had been obvious before.