Continuity mistake: On the video of Ian supposedly killing Alison, we see her arm fall to the ground with her "Alison" bracelet visible. But in a later scene where Emily watches Ian put his bag in the athletics room, we cut back to the video and Alison's arm suddenly has a sleeve covering up her bracelet. When we see the video again later in the series, her bracelet is visible again.
Continuity mistake: Duke is wearing an extra shirt, and his hair is longer then it was, despite continuing the scene from the end of season 2.
Continuity mistake: Ava spills Coke on her blouse and creates a big circular stain. As she walks to the bathroom, the stain becomes a long narrow one. When she is leaving the pizza place, the stain is still narrow, but much shorter. (00:21:00 - 00:22:00)
Continuity mistake: In the morning, Annie comes into the kitchen and says hi to her niece and nephew. Her jacket is alternately buttoned or unbuttoned. (00:39:30)
I Haven't Told You Everything - S1-E1
Continuity mistake: In the first episode, the pilot of the plane's shoulder rank changes from stars to stripes, back and forth, repeatedly from scene to scene.
Continuity mistake: When Alex is in the evidence room she has her arms folded in one shot and her hand instantly on the table in the next.
Continuity mistake: When Gary is at the end of the table talking about Golf, he's actually seated in front of the table as seen by how he grabs his cup in front of him. In the very next shot, he's no longer sitting in front of the table and is sitting past it.
Continuity mistake: When the hostages try to get some rubble to catch fire, they find that everything is covered in some flame retardant stuff. Yet, in the very first episode one of the very first things they do is to make a small fire to get the fire alarm going.
Continuity mistake: When the bomb under the bus is being defused, it's counting down and beeping once every second. We see the timer at 0:45, then cut to the face of the woman defusing it - counting the beeps when we cut back it should be on 0:45, but it's jumped up to 1:06. Camera pans down to her face, then back to the bomb, and it's now on 0:43, but going by the beeps it should be on 0:36. We cut away again for 5 more beeps, cut back and the bomb's only just ticking onto 0:41.
Continuity mistake: In episode 3 or 4, one of the characters is knocked out and lying on the floor in the Russian sub. He is on the 'left' side of the shot most times he is shown, but occasionally he's on the right.
Episode #3.2 - S3-E2
Continuity mistake: Dalton and the terrorist are fleeing from the building when Locke arrives and hits the terrorist who has backed into the street with his car, thereby saving Dalton. The terrorist flies over the hood and lands behind the car in the street, never going anywhere near the driver's side of the car. Locke reenters his car to a broken driver's side mirror.