Chuck Versus the Wookie - S1-E4
Continuity mistake: When the DEA agent Carina is running on the beach, she is wearing a white undergarment under her short black dress. Moments later she pulls off the dress and we see that she is now wearing a black bikini. (00:25:59 - 00:26:25)

Chuck Versus the Break-Up - S2-E3
Continuity mistake: When Morgan cuts the power to the home cinema room at Buy More and the angry black guy storms out, the circuit breaker box is still open. Yet, when he grab hold of Morgan a second later, the box has closed itself. (00:12:20)

Chuck Versus the Imported Hard Salami - S1-E9
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. (00:37:00)
Deliberate mistake: Although it is later revealed that Sarah is the intruder, the person fighting is male.
Chuck Versus the Gravitron - S2-E8
Revealing mistake: In the scene where Ellie is testing her Thanksgiving turkey by giving Morgan a piece, when she throws it in the trash he says 'no no no Sarah.. what are you doing!', which is the actor's name (Sarah Lancaster), not her character's. Maybe edited in some versions. (00:09:40)
Chuck Versus the Fat Lady - S2-E7
Factual error: When Chuck and Jill recover Guy LeFleur's hard drive containing the list of Fulcrum agents, General Beckman says that the flash drive is encrypted with a 512 bit AES cypher. She then goes on to state, "the computer is trying every possible key against the encrypted data, " i.e., a brute force hack. However, it would take the fastest supercomputer in the world longer than the existence of the known universe in order to crack even a 128 bit AES encryption (and a 512 bit AES encryption has the number of possible keys of a 128 bit AES encryption, raised to the fourth power). In a previous episode, Chuck refers to the computer in Castle as having a "30 teraflops" speed, which is far less than the current fastest supercomputer. General Beckman instead says it will take only hours or days. (00:26:10)

Continuity mistake: Sarah's stilettos transform into flats when running after Chuck through the pool. (00:34:50)
Chuck Versus the Broken Heart - S2-E18
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.
Suggested correction: Obviously Devon was unconscious and did not show up to the surgery. There was no mystery surgical team. Hospitals have on-call or standby surgeons for emergencies or when the primary surgeon is delayed and the surgery is critical, as in this case. Because the substitution had just occurred, the patients' paper chart would probably not have been updated yet, so Devon was still listed as the surgeon and the killers went after him.

Continuity mistake: The size of the laser aimed at Chuck during the rooftop standoff changes in every shot. (00:33:35)
Chuck Versus the Ring - S2-E22
Continuity mistake: In the wedding scene in the opening wide shot we see Morgan and the mic on stage before the actor goes on stage a good two minutes later.
Chuck Versus the Predator - S2-E17
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. (00:02:10)

Continuity mistake: When Devon arrives to the CPR course for the Buy More employees he brings a CPR-doll and puts it down on the table. Yet, a second later it's right back in his arms in the same seemingly uncomfortable position as before.
Factual error: In a scene in "Chuck Versus the Anniversary" (S04E01) that aired Monday September 20, 2010, Chuck is supposedly riding a Los Angeles city bus. But the buses pictured are NYC buses. (00:14:05)

Chuck Versus the Sensei - S2-E9
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. (00:05:50)
Chuck Versus the Beefcake - S2-E15
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.
Chuck Versus the Truth - S1-E8
Continuity mistake: Big Mike is talking to Morgan. When looking at the banana, it changes at the cuts in this scene.
Chuck Versus the Fake Name - S3-E8
Factual error: When they first bring Grueber into Castle, Sara states that "he is one of five people who can hit a target from half a mile away." Half a mile is 880 yards. Basically every person who has graduated from (or likely everyone who has been selected for) sniper school in any military in the world should be able to do this. (00:05:20)

Chuck Versus the Fear of Death - S4-E8
Continuity mistake: Near the end when Jeff and Lester confront "Greta" in the cage she pulls out her knife. Jeff attempts to disarm her but she cuts off his tie. She cuts it very close to the top, leaving very little around his neck, but when it cuts back to him after showing the piece hit the floor there is much more tie left.
Chuck Versus the Gravitron - S2-E8
Continuity mistake: As big Mike storms the fulcrum agent leader, the gun goes flying out of his hand, but when hes seen lying in the pile of boxes, the gun is back in his hand.

Continuity mistake: During the car chase, the NSA's black SUV rams into Chuck's little car. The front license plate breaks off and is hanging on by one corner. When it's backing down the stairs, the plate has somehow reattached itself perfectly to the bumper. (00:29:20)