Continuity mistake: In the scene where Layla passes the note to Zack, he has a gray shirt on which is not tucked into his pants. Later, when Clayton is following him the gray shirt cannot be seen. (01:22:20 - 01:23:10)
Continuity mistake: While searching Zack's bloody jacket for the note Layla passed Clayton's hand gets bloody. However, after reading the note he puts his hand to his mouth and there is no blood on it. (01:26:00)
Continuity mistake: When Clayton is a "prisoner", rips and tears in his shirt appear and disappear throughout the entire scene.
Plot hole: There is absolutely no point in getting James involved with Layla for Burke. She could have given him the program, why get someone to sabotage his own plan?
Audio problem: When the recruits are pulled out of bed at 06h00 in the morning for a run, the running instructor walks past Colin Farrell and Bridget Moynahan asking if everyone is ready. When we see a long shot of the instructor, his mouth opens but no sound comes out. We only hear his words "Let's go!" when the camera is on Colin, who is making gestures towards his mouth.
Continuity mistake: When Burke circles CIA on the newspaper at the bar, the newspaper is folded in half and positioned so Clayton can read it. A scene later the newspaper is not folded in half and it's positioned so Burke can read it. (00:06:45)
Factual error: When James jumps on a Metro train at Union Station after killing Zack, the Metro conductor's voice is heard to say, 'Red line to Shady Grove. Next station Dupont Circle.' On the red line going towards Shady Grove, the next stop after Union Station is Judiciary Square. Dupont Circle is actually the fifth stop after Union Station.
Continuity mistake: When Al Pacino is being shot, there is no blood on his top, just a bit of smoke.
Visible crew/equipment: In the scene where Layla drives her VW through the gate you can see a camera lens (a bright circle) in the passenger seat of Clayton's truck. This is the angle used for a brief moment from his view when she crashes through the gate. (01:32:20)
Plot hole: Wouldn't the scanner that she puts the coffee mug through be able to detect the USB connector in the bottom?
Factual error: When Burke is explaining the exercise about following the 'rabbit', in one of the shots on the ground there's a map of the world (I think it's a political map). So, the big yellow area in Europe looks very much like the Soviet Union which doesn't exist since 1991, besides, there's no Crimean Peninsula in the Black Sea on that map.
Character mistake: Before using the handgun, Clayton saw that it had bullets in the magazine. Later, his bullets caused sparks and ricochet sounds from hitting concrete and steel when fighting Zack. After Layla accused him of being a double agent, Clayton challenged Burke to explain what's going on, and deflected most of Burke's lies but then seemed most confused - despite his knowledge to the contrary - by Burke's claim that Zack is alive because Clayton's gun was shooting blanks. (01:37:10 - 01:38:35)
Other mistake: When Clayton shoots Zack, both the position of the gun and the location of the blood on Zack's jacket are about mid-torso on the left side. Yet not only is Zack shown to die in only 15 seconds, but Clayton does nothing to check pulse, breathing, pupils, or even the wound, which is inconsistent for this trained agent who didn't want to kill his friend; instead, he retrieves a paper from Zack's pocket and flees. (01:25:46 - 01:26:27)
Other mistake: Burke told Clayton that Langley's computers don't have printers. However, while Layla sits in Sharon's cubicle, just after Clayton walks by we see a printer behind Sharon on her desk. (01:09:13)
Plot hole: Why would the CIA ask Layla to test its security by stealing a real and harmful computer virus (the real Ice 9)? Unless Burke had somehow fooled the CIA into thinking what Layla was stealing wasn't real, but in that case she could have had Layla given him ice9 himself.
Continuity mistake: When Layla is trying to get away from Clayton in the car chase, she goes to pass a blue car behind a white truck. It cuts to a shot from inside her car and the white truck is there, but no blue car. Another car is coming the other direction and she has to yank the wheel. She should have been creamed by the blue car, but wasn't because it disappeared. (01:32:10)
Continuity mistake: When Clayton is hiding behind the SUV a shot from behind shows him peeking his head out to look at Layla. It cuts to a shot from the front where most of his torso is out from behind the SUV. Then another cut to behind shows only his head out again. (01:21:05)
Continuity mistake: After Colin Farrell checks out the Ice9 data on his laptop PC and calls Bridget Moynahan, he puts his Spartacus disc into the computer's drive. In the next shot, the laptop PC is no longer on his lap.
Continuity mistake: After getting shot, Zack touches the bloody jacket with his left hand. When he dies there's no blood on the fingers he touched it with. (01:25:45)
Continuity mistake: In the final scenes Al Pacino shoots at Colin Farell until the slide locks back on his pistol. When they make it outside there is a shot of the pistol with the slide fully forward just before they cut to another shot of him releasing the slide from the locked back position to the fully forward position.
