Near the beginning of the movie a car arrives to the airport. The shot from the inside of the car reveals an inspection sticker on the windshield that expires in 2004. The latest an inspection sticker in 2001 could expire would have been 2002.
During the overview of the Newark airport in the beginning, an air-traffic controller can be seen wearing a blue lanyard displaying, "Transportation Security Administration" with an American flag displayed after "Transportation". These were issued post-September 11, 2001 as the Transportation Security Administration was formed under the Aviation and Transportation Security Act, which was signed into law on November 19, 2001. Most 2001 roll-out supervisors at the TSA have these lanyards for airport identification cards. An ATC could own a lanyard as it is understandable that the lanyards would be distributed throughout the airport operations personnel.
Just before Captain Jason Dahl announces a delay in take-off, an Air Canada plane is shown taxiing behind Flight 93. It's an Embraer Jet which the airline first started flying in 2005, in a color scheme first introduced in 2004.
When auditing the recording of a transmission from American Airlines Flight 11, the reviewer repeatedly listens to the crucial portion, rewinds the tape, and listens again. But as the sounds play, the reel moves only a small fraction of a turn, while the rewinding covers several times that distance; yet the reviewer supposedly always ends up back at the same point in the recording.
In the beginning of the film when the hijackers are leaving their hotel room, the one in the front is wearing a horizontally striped polo shirt. The shot then cuts abruptly while they are walking down the hallway and the same man in now in a button down shirt and a sport coat.
When the captain turns off the fasten seat-belt sign, the stewardess walks through the closed curtain, turns and closes it again, says her line at the front of the plane and turns back towards the curtain which is now fully open.
Near the end of the movie, when the passengers are fighting for control of the plane, the main stewardess is shown in many shots as the passengers move to the front. Almost each shot of her shown has her hair is arranged in a different way.
In one scene the hijacker flying the plane puts it into a steep dive but when the camera shows the passenger cabin the plane appears to be angled upwards as if in a steep climb and the hijacker watching the passengers from near first class if leaning backwards (towards the cockpit) to maintain his balance also indicating a climbing deck angle.
Once the passengers on the plane are hearing of the WTC attacks, the stewardesses at the back start hearing the passengers talking and start reacting. However, between shots, the positions of the stewardesses change very noticeably. One is in front of the rest of the stewardesses at the back listening to the passengers but in the next shot, she's in the far corner tucked up against the door of the plane hiding. In the next shot, she's back to her original position.
When Ziad Jarrah rolls the plane to knock the passengers off balance one of the air stewardesses Sandra Bradshaw is seen falling to the floor at the rear of the plane but in the next shot she is seen struggling to get up in first class then a few scenes later she is strangely back at the rear of the plane getting up.
During the final scene of the movie, where the cabin is inverted upside down and the oxygen masks eject from the ceiling, you can clearly see that some of the cabin ceiling panels are missing and you see tubes and wires in light blue and red colors revealing the set.
Various goofs exist at the start of the movie while the passengers are arriving at the gate at Newark Airport which reveal the shooting location to be the domestic departure gates at Stansted Airport, Essex, UK. These include the BAA signage, the seating at the gate (17), the rail link to the international departure gates (seen through the glass at the security checkpoint) and a "2 for £25" advertisement on the passenger walkway towards the gates.
A number of passengers are seen making phone calls from cell phones, but in reality, only two people made calls from cell phones during the last few minutes of the flight - Edward Felt and CeeCee Ross Lyles. All other calls came from in-flight phones.
When showing the Surface Movement Radar (SMR) at Newark, the aircraft is labelled as UA93 which is the IATA code for United. Air Traffic Control uses the ICAO codes and therefore the correct label for the flight should be UAL93. The correct code is shown in all the scenes at Boston and New York centers.
Boston Air Traffic Control Center refers to American Airlines flight 11 and United Airlines flight 175 as 'American eleven' and 'United one seventy-five', but New York Air Traffic Control Center refers to the United flight with 'heavy' succeeding the call-sign, although both aircrafts are Boeing 767-200s.
During first officer's preflight walk around, the aircraft has Rolls-Royce RB211 engines. In fact, all United 757's are equipped with two distinctive Pratt & Whitney 2040 engines. The engines alternate between Rolls Royce and Pratt & Whitney during exterior shots of the 757.
In several scenes, the altitude indicator ("artificial horizon") shows the aircraft in a climb, while shots through the windscreen show the aircraft in a dive. The scene is shot at a downward angle furthering the illusion of a dive.
Despite the aircraft being flown manually, on the Primary Flight Display in some of the scenes, "CMD" text is still present (possibly taken from another aircraft). It means the plane is still under the control of the autopilot.