When Captain Steele retards the power levers upon reentering the cockpit, you see four of them on the center pedestal. The aircraft that has been shown all along up to this point has only two engines, not four.
When Chloe listens to the voicemail left on her phone by her father, you hear the sound of the crash immediately following the Captain saying "one zero zero zero." However, when the crash was shown as it occurred, sixteen seconds elapsed between the Captain saying "one zero zero zero" and the impact.
The plane loses a part of the right wing in the mid-air collision, but in later scenes of the plane returning to land at JFK, it appears that the right wing is undamaged.
The school bus comes off the bridge whilst Chloe is walking under the underpass, however the disappearing event took place whilst Chloe was in the Mall. The driver-less momentum of the bus would not have it coming off the bridge substantially after the disappearing event.
At one point during the movie, Ray says he's unable to land the plane on water as the plane's nose isn't lifted since it's falling. Later, at around the 1:30 mark, we see a visual of the plane flying with its front pointing up.
Captain keeps saying he barely has fuel to go to JFK. However, there are at least five available airports on route NYC - London that are closer than JFK, Gander in Canada being the emergency airport on all transatlantic flights.
After chatting with the reporter in the cockpit, the pilot picks up his microphone and says, "JFK Tower, do you hear me? I Need a clear runway. Repeat. I need a clear runway." But he doesn't identify his flight, so the tower wouldn't know who was calling. A seasoned pilot trusted with an international route wouldn't make a mistake like this. Radio protocol would be automatic.
When Captain Steele is approaching the mid air collision, the plane issues a TCAS (Traffic Collision Avoidance System) Alert. The captain then tries to contact the other pilot. In real life the TCAS already tells both pilots what action to take such as dive or climb. Due to the very high closing speeds of approaching aircraft, there is no time to contact the other aircraft. It's akin to calling a car ahead of you on the highway to avoid a collision. If he obeyed the TCAS, he would not have collided with the other plane.
Normal procedure when a fuel tak is punctured or a fault is detected is to use the plane's controls to pump the fuel from the damaged tank into the undamaged tanks using the cross flow control. However this is not done. Also if you have a fuel leak near an engine that engine would be shut off to minimise risk of igniting the leaking fuel.
There are at least five planes involved in this movie. One Airbus A300 (wide-body--two aisles) on the gate, when passengers boarded the aircraft. One Boeing 767 (wide-body) every time the camera shoots the plane from outside when it is flying. One Boeing 747 (wide-body--two decks) when the camera shoots the flight deck (cockpit) from outside. One Boeing 737 (narrow-body--single aisle) when the plane performed emergency landing. And one Boeing 717 (narrow-body) when the plane is fully stop and all the passengers are outside.
Shasta pulls out a gun in the midst of the chaos between all of the panicked passengers, something that is virtually impossible to bring onto a flight anymore in a post 9-11 world. Later the pilot states that the gun belonged to the Air Marshal on the flight.
The first time Hattie addresses the plane's passengers, she speaks into the earpiece of the phone.
After the majority of shoppers disappear in the mall and leave behind their clothes, children's clothing begins to fall from the ceiling which makes no sense.
When Chloe and Buck are sitting down and talking in the airport, a young female extra peeks around the pillar probably waiting for her cue to cross. She then steps back out of frame. In the next shot, she's finally crossing.
When Captain Steele is seen entering the flight-deck for the first time, the camera shows the aircraft's instrument panel. The landing gear lever is in the up position, this would only occur while the aircraft is in flight.
When the instrument panel of Charlie 1581 is shown, it is very evident that this is a shot taken while the aircraft was sitting on the ground with the engines off. Obvious indicators are: The airspeed reads zero, The altimeter indicates around 1000' MSL, all of the engine gauges read zero, the gear handle is down and the three green gear down and locked lights are on, the Captain and First Officer's attitude indicators differ by about five degrees, all three engine low oil pressure lights are illuminated, and so much more.
A news report on a television in the mall immediately begins to announce the events that are unfolding merely seconds after the rapture commenced.
When the rapture begins in the shopping mall scene an empty car crashes through the doors nearly killing Chloe and the whole time this is happening the engine is revving, something that requires the operation of a human.
In the film it is said there are no other planes and yet after 92 minutes a very clear shot of a tail plane is visible crossing the screen from left to right.
Pilots never wear their jackets/blazers during the flight as they can be restrictive when reaching the overhead panel etc, as well as being generally uncomfortable when sitting for long periods.
When the passengers begin to evacuate the aircraft down the emergency slide, the flight attendant says to the approaching passengers, "One at a time." This is completely against evacuation procedure and training. Flight attendants will move passengers out as rapidly as they can to get them through the door, literally pushing them if need be. As an example, Airbus demonstrated this procedure (which is required for certification by the aircraft manufacturer and by the airline) by evacuating 873 seated and belted passengers and crew in only 78 seconds. You could not even begin to do that if the passengers went down the slide "one at a time."
When Captain Steele parks his car at crew parking lot and meets up with his girlfriend, she has her standard crew luggage, but he does not. As an airline captain, not only would he have a standard roll aboard bag, but he'd also have a pilot's chart case with all the maps, approach plates, and directories required. In other words, two pieces of luggage. Surely, he wasn't going to the U2 concert in London in his pilot's uniform.
The pilot does not use standard protocol on the radio for declaring an emergency, saying "mayday" twice at one point and once a second time, instead of the required three times. Also, in an emergency, he would not fly the plane three hours back to JFK but land at the nearest available airport, which would be in Canada.
Nicholas Cage's character goes into the airport for a multi day trip with no luggage even though the stewardess he is flying with is smart enough to have packed carry-on luggage.