In the closing scenes, the aircraft is not a Boeing 747 as depicted in the rest of the film. It is actually a Boeing 737-400, wearing the markings of Alaskan Airlines instead of the correct Trans-Con scheme.
On the final approach, the controller says the plane was "too low", while the VASI lights on the left to the runway show the plane to be too high (two white strips instead of two red ones).
The ILS computer is destroyed during a shootout, but Martin is instructed to perform an ILS approach.
When the plane stops at the end of the runway, engines 3 and 4 are running. However, just a few moments earlier, engine 4 was shut down due to low fuel.
The display shown during the ILS approach is the Flight Director which is controlled by the autopilot. Earlier, it was said the autopilot was out of order.
Flaps cannot be controlled from the cargo hold. Furthermore, deploying the spoilers in flight would also cause the aircraft to slow (not just descend as depicted in the film).
Anytime the gun goes off inside the aircraft when it hasn't hit a body first, it will puncture the thin skin of the aircraft causing explosive decompression. Even if the bullet hits a body first, it still has a chance to go through and puncture the skin of the aircraft.
In the 85th minute the hijacker throws the passenger out of the plane. In reality, once the door is opened, they both would have been sucked out.
VORs are ground transmitters that work one way. There is no way to use the VOR receiver to transmit information like the Morse code sent by Martin.
When the fuel tank gauge is shown, the letters "EGT" appear among the bars. Actually, the shot shows the engine exhaust gas temperature gauge instead of the fuel gauge. The two bars turning red would usually indicate an engine fire.
When Elliot is on the air phone in the cockpit, there is no cord on the phone.
At the beginning of the flight, the cockpit windscreen glass seems to be missing.
When the pilot is dead and being dragged from the cockpit, the first aid kit is labeled "FAKE" in big red letters.
In the 22nd minute it is unclear why a US airline would have toilet signage written in Chinese.
In the 13th minute the new flight attendant has no 'wings' pin on his uniform.
The ambulance toward the end has no ID/unit number.
In the 87th minute the dead man in the ATC can be seen moving.
In the 72nd minute when Martin and Jessica push the shipping out of the plane, it is unclear why it explodes in midair over the ocean.
The city they fly over on approach to SeaTac is not Seattle.
Supposedly set in part at Seattle-Tacoma International Airport, but neither the airport interior nor the surrounding mountains resemble SeaTac.