Factual error: A flight manifest would never state on its seating chart that an armed U.S. marshal was on board as it gives away that person's identity and puts everyone on board in danger.
Factual error: The crew sent to board the ill fated jumbo jet is in the "Remora", which is clearly a modified F-117A Stealth Fighter, but retaining the same dimensions. It would be physcially impossible to fit that many people and such a spacious cargo hold into a plane that size with the engines. In fact, with the additional weight, the engines would have to be even bigger for it to operate.
Factual error: Computerized maps throughout the movie show the plane heading due west past Spain and Portugal from Athens to Washington, D.C. Aircraft follow great circle route; although Athens and DC are similar in latitude, the shortest flight path is north over Scandinavia. No commercial air route between Athens and the East Coast fly over Spain.
Revealing mistake: When the Oceanic 747 attempts to make its first landing, you can tell that the 'hole' on the side of the aircraft is simply painted on.
Continuity mistake: When Grant goes down to the main cabin and is looking around for the sleeper, the fringe of his hair goes from up and pushed back to all hanging down without him touching it.
Continuity mistake: Near the end of the movie, when Grant takes control of the airplane and lands on his second try, you can see the inner engine on the left wing (right to us) fall off and catch fire after impacting with the smaller parked planes. In the next shot, which happens quickly, you can see the engine is still in place and not damaged at all. In the next shot, it's gone again and the wing is on fire where the engine was.
Factual error: When the bullet is fired through the aircraft window there would be no possible way that Grant would be able to hold on for that whole time as the plane is travelling up to 600mph and also his temperature will lower immediately, which would cause weakness.
Continuity mistake: When the girl goes down in the plane's elevator, you can clearly see the phone to her left (our right) has no light. In the later parts of the movie the phone becomes a very significant tool and now has a light on it. (00:12:03)
Revealing mistake: Because the hijacked plane is carrying deadly chemicals, the military officers at the Pentagon plan to takeoff urgently within 1 hour. Yet when they reach the airfield you can see palm trees and mountains in the background. If the meeting was in Washington DC, they'd need to takeoff from a nearby airfield. 1 hour is not enough time to get from Washington DC to any airfield with palm trees and mountains. This scene was probably filmed in California.
Factual error: When John Leguizamo is surveying the cabin for terrorists and reporting back to Kurt Russell, he says the terrorists are carrying 9mm Skorpions. The Skorpion IS produced in 9mm Makarov and .380 Auto versions, but those weapons have straight magazines, not curved ones. The terrorists' Skorpions have curved magazines, which denotes the weapon being chambered for 7.65 Browning.
Factual error: As they are disarming the bomb, the hard drive on the bomb has no cover. A speck of dust would destroy an exposed hard drive and it would never be used exposed like that. As Cahill is a design engineer and quoted as being able to build computers, he should know that this hard drive is wrong.
Plot hole: The entire movie is a major plot hole. It's revealed early that Naji Hassan himself organized Jaffa's capture and so it follows that Hassan has no interest in the latter's release. With the nerve gas already smuggled on board the plane and the willingly suicidal Demou in place, the hijack was totally unnecessary. Demou could have set off the bomb as the plane came into land. Rather than draw attention by the hijack, Hassan could've stayed behind and made propaganda from a safe place minutes before.
Factual error: Kurt Russell lands the 747 at Frederick field and during the rollout the plane's left engines collide with parked aircraft and it finally runs off the departure end of the runway into a sand drag. While it is true that the 5000 ft runway at Frederick field is too short for a Boeing 747 in reality there would not be aircraft parked so close to a runway at any airport, and we know that the 747 did not veer off the runway since it struck approach lights at both ends of the runway.
Factual error: Throughout the movie the Carrier mentioned that will send fighters to attack the Highjacked airliner is the CVN-69 Uss Dwight D. Eisenhower. You can see CVN-69 on the briefing screen at the NMCC. However after the SECDEF gets the pic of the bombmaker they cut to a scene of the carrier getting her fighters ready and the carrier is now the CVN-74 Uss John C. Stennis. You can see the 74 on the tower of the carrier.