Factual error: The premise of the film is swapping the faces of the Hero and Villain. We can see the whole face of Sean Archer is intact in a water tank, which includes his eyelids and lips. When Castor Troy wakes up and confronts the doctor, despite his face being missing, he still retains eyelids and lips, which isn't possible as they would be missing. This should result in Castor having exposed eyes and teeth. (00:46:47 - 00:48:08)
Factual error: In the scene in the hall where there are is a circle of mirrors where Castor and Sean engage in a shootout, there is a mistake as the FBI agent fires at Castor. The FBI agent is holding an M16 or M4 assault rifle with an M203 40mm grenade launcher. He fires two consecutive shots within a second of each other. This is impossible as the M203 attachment only holds 1 shell at a time and would take at least 5 seconds to grab another round and reload and fire again.
Factual error: Never mind that their faces are taken off (and a fast recovery time, as well), but John Travolta is tall with broad shoulders, Nick Cage is short and thin - how did all this get changed? I know plastic surgery is possible, but these two men would need intensive plastic surgery and would need months or years to recover, not several hours.
Factual error: In reality, a face transplant like this couldn't work for multiple reasons. Primarily because of blood type, with Castor (Cage) being AB and Sean (Travolta) being O Negative. Organ donors and recipients need to have the same exact blood type for transplants to work, otherwise the recipient's body will reject it even with medication. In addition, intensive surgery is needed to connect a donor face to a recipient (ex. Connect blood vessels), which takes more than several hours.