ATC says they are lined up to land on runway 12, but the actual landing occurs on runway 16.
Besides the fact that the stewardess fires an Uzi toward a cockpit (and all the other gunfire that occurs on the plane) without compromising the pressure hull or damaging any cockpit equipment, she starts out firing 2 or 3 shots in single shot mode and then lets off an automatic burst without switching to full auto. As they show the bullet holes appearing in the terrorist and he crumples, a few rounds of the burst continue after he has fallen, and she is still firing directly into the cockpit, but nothing happens to the cockpit windows or instruments.
NSA Agent Quinn orders the launch of F-15s to intercept the airliner. The planes shown launching and in flight are in fact F-16s.
When bad-guy accidentally opens the jet's passenger door in flight (impossible BTW), he is blown out and is dangling by his fingers. The flight attendant walks up and hits his hands with a non-standard coffee pot. How come she isn't pulled outside too? She just walks away as if there was no air currents at all.
The air traffic controllers were sitting in front of computer screens instead of radar screens where they should have been.
An SR71 BLACKBIRD would never be employed to do this for a number of tactical reasons. It's hydrazine fuel expands too much on the ground and forces the SR71 to take off with low fuel load and being refueled in air by a similar aircraft like the 747. It is much larger than a 747, It flies too fast to rendezvous with a slow 747. There's no room inside for a rescue team. It's not quiet so it can't sneak up on the other plane. It's black hull is highly visible from a distance. That vertical interface personnel tube would have caused the 71 to go out of control. The jet-wash from the 747 would have totally swamped the 71.That's why they fly well below the re-fueler jet plane and a boom fuel interface is lowered down to it.
Ground control tells Kelly to change course from a heading of 619 to 502. Neither of these headings is possible since the highest compass heading is 360.
When they dump the fuel the two control boxes have wires hanging out of the boxes and the wires are connected with household wire nuts which would never be used in that type of wiring.
When the bad goon was hanging outside the emergency exit, the FA was hitting him with the coffee pot, you can see black wires attached to the bad guy as he was hanging onto the plane.
The NSA agent tells the fighter plains to get behind the jet liner and "light them up" with their attack radar to get the pilots attention. The pilot of a commercial plane at that time would not have instruments available to him to show that he was being targeted.