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 loaded by a third party.
Other mistake: In the cabin Jeremy Renner looks up and sees the name Jason Bourne carved into the wood. Jason Bourne was one of the many aliases of David Webb - he wasn't given the name Jason Bourne until he completed his training.
Continuity mistake: They are shown boarding a Boeing 767, which is a twin engine plane. We're then shown a four engine plane flying off to Manila.
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.
Factual error: American Airlines does not carry passengers from America to the Philippines, nor do they operate any 747s.