Factual error: When the Delta Force lands on a beach, prior to their assault, their landing craft is lit up like a christmas tree. The commandos wear dark uniforms and have blackened their faces, but they also carry bright white ropes around their chests. Some of them are scuba-divers, wearing yellow oxygen-tanks. In short, in the real world they would have been spotted within minutes.
Continuity mistake: When Chuck and his compatriot are escaping from the terrorists in the Greek Orthodox Church van we see Chuck leaning out of the side of the van until the sliding door is hit with three shots in a near straight line, however, the next time we see the side door panel it is undamaged until subsequent shots which show a square grouping of four holes instead of a line of three.
Continuity mistake: During the scene where the hijackers have demanded all passports be collected by the flight attendants, pay close attention to the part where right after Ben Caplan is called to the front. Right behind Caplan's seat is a bald guy with glasses who hands Ingrid his passport. A few minutes later, Ingrid is approached by 3 Marines stating that they don't have passports and instead have Navy Id's, and right as she says, "Put them away", the same exact bald guy with glasses a few rows back can be seen holding his passport above his head.
Audio problem: During the scene where Abdul is having Ingrid read the names of the Jews to be called up to first class cabin, Moustafa is arguing with the two nuns about another passenger who claims he is not Jewish. The nuns are telling Moustafa that "this man is telling the truth" and you can hear Moustafa yelling back, "Sit down, we know what we are doing" at least twice, but on both occasions it is very clear his lips don't match what he is saying.
Revealing mistake: 10 minutes into the movie, the hijacker is at the cockpit cabin door and forces the stewardess to have the captain open it. If you look behind the hijacker at the main cabin door, you can see light coming through it on the upper right each time they show him from the front. It's a sealed plane door, there wouldn't be any light coming through.
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