During the hijackers' flight training, a pan shot shows an Independence Air jet in the background. Independence Air did not exist in 2001.
In the scenes in Pakistan and Kenya, cars were left hand drive (this was probably due to the scenes being filmed in Morocco, which drives on the right.)
One of the main characters, John O'Neal, speaking to Ambassador Bodine, says that the Hadhramaut region is "northwest Yemen". Actually, Hadhramaut is southeast Yemen.