Continuity mistake: In the scene where Sarah and Chuck find the suspected bomb, Sarah initially tries to disarm it by removing the numeric key pad under the display. She leaves the keypad off when she goes over to talk to Chuck. In the shots where the characters are talking, the keypad remains off but every time the shot changes to a close up of the suspected bomb the keypad is back on, under the display.
Continuity mistake: In the scene with Orion working at his computer in Hong Kong and the Fulcrum agent is coming, he is watching Chuck, but he hears them, closes the window and its blank, but then the immediate next shot the screen shows Chuck still, and then the next shot it is black again.
Factual error: A recurring mechanism in the series is if the power fails the prison cells that are magnetically locked open immediately. No magnetic locks are designed like this. They would fail their initial purpose which is to provide physical security. If a power outage occurs it would take hours before the locks would be released.
Continuity mistake: The yellow pen that John Casey stabs into Ty Bennett changes between shots after Ty pulls it out. As he rotates it in front of the camera we can see that the bold BUY MORE logo is only printed once. Still in the very next shot, not only has the text changed direction (reading from the hat-side to the tip-side now), the logo have also appeared in front of Ty.
Continuity mistake: There's a noticeable jump cut after Jill separates from Sarah - we see a cubicle, with a Fulcrum agent getting up and running off to the left, leaving his chair spinning slightly. He exits, then just before Jill enters (apparently in a continuous shot), the chair suddenly rotates to a different position and then stops.
Continuity mistake: Sarah is making Chuck a frozen yogurt using a banana and a knife. Take notice when Sarah cuts up the banana, the slices are disorganized while she is talking to Chuck. However, when Sarah decides to pick up the slices of banana, the pieces are now nicely organized.
Revealing mistake: When Sarah and the Triad chick are fighting, Sarah is thrown through the window of a late model Dodge. When she is thrown through the window, it breaks into large shards, indicating it is not made of the safety glass which is used in all car windows. But then, while they are fighting in the car, all the glass inside is small pieces of safety glass, not the shards.
Continuity mistake: In the series finale "Chuck versus the Good-Bye", Chuck and Sarah are in the Wienerlicious waiting for Quin to show up, Sarah begins rearranging the cups. There are three stacks of cups, and after she has set the third stack down, the camera cuts and she is now just reaching for the third stack. (She moved the third stack twice.)
Plot hole: Casey needs to get Devon's hospital keycard in order to get into the secure holding area to plant the listening device into the pacemaker before it's implanted into the terrorist. They obtain the key-card by stunning him at his bachelor party and see Casey using it to access the storage facility, backed up by Chuck and Agent Forrest. We then see the terrorists scanning their leader and detecting the implanted bug - Devon is listed as the surgeon. Immediately after this, we cut to Devon waking up from his bachelor party with his keycard missing. None of the three agents involved in planting the bug could possibly have handled the operation, no other agents are mentioned as being present and, as the break-in occurred during the daytime, the staff of the busy hospital would have noticed had an unknown surgical team suddenly taking over one of their operating theatres. So Devon apparently got into the hospital with no key and did the operation while completely unconscious.