Continuity mistake: They are shown boarding a Boeing 767, which is a twin engine plane. We're then shown a four engine 747 flying off to Manila.
Factual error: The rifle Aaron Cross is shooting is a bolt action rifle, but it's shot semi-automatically. (00:33:46)
Other mistake: When Aaron Cross watches the wolf pack take down a caribou early in the movie, and we get a through the scope view. Amazingly he does this with the lens covers closed.
Factual error: American Airlines does not carry passengers from America to the Philippines, nor do they operate any 747s.
Factual error: Aaron Cross claims he got into the Army because his recruiter lied on his application and added 12 points to his IQ so he would meet the minimum. The problem with that claim is the military does not take your IQ into consideration for enlistment. The military uses the ASVAB to determine academic qualification, and it is not a measurement of your IQ. Also, in order to prevent dishonest recruiters from altering test scores, recruits are tested in a neutral location and have their scores recorded by a third party. (01:21:15)
Plot hole: The tracker chips that the program participants have surgically implanted in their legs make no sense: (1) Implanting an RF device in an agent who is going undercover in North Korea, Pakistan, Iran etc. is a very efficient way of blowing his cover. (2) The drone pilots are unable to imagine that the agent may remove or shield the chip, despite knowing that these agents are super-intelligent and resourceful. (3) Why does killing the agent switch off the chip? Even if he's blown apart by a Hellfire missile, the chip should still keep chirping away, safe inside the lump of meat that's left.
Other mistake: During the workplace shooting scene, a lab doctor/technician is shown banging on the door, pleading to be let in. He has two blood stains on the back of his lab coat, apparently from being shot. However, his demeanor, his ability to speak and physically move is not congruent with having been shot twice in the back. Moreover, when he is shot, he is shot three times but, when he falls over, his lab coat has five blood stained holes. (00:45:07)
Continuity mistake: When Aaron steals a Piper Navajo, you see him piloting, there's a wing tip, then in the outside shot of the Navajo, the wing tip isn't there any more. (00:48:18)