Plot hole: The convicts remove the radar transponder from the Conair aircraft and put it aboard a tour plane to distract their pursuers. That won't work. By law the tour plane will have a working radar transponder of its own, and two working transponders that close together will show up on radar as a collision. Air traffic controllers would immediately alert emergency services who would, obviously, wonder how two aircraft that had collided had managed to stay in the air. Nobody disconnects the first transponder - Pinball carelessly tosses the second transponder under the rear seat of the aircraft (the implication being that it continues to operate, perhaps on backup battery power). He doesn't disconnect the original transponder either - Swamp Thing, a skilled pilot, does that. There is no time for him to do any of this before he is stopped by the female security guard anyway.
Plot hole: When Larkin runs towards the crane to use it to stop/damage the business jet, he totally outruns it. In the beginning shot he is right next to it (alongside), and as the plane accelerates he starts running, he makes it to the crane, then in one shot from the front you can see how close the plane is already to the crane, and in the shot from the side you can see that it's farther away again but much faster, with Larking already sitting in the crane. Cindino is in a rush, they taxi/accelerate as fast as they can. It's impossible to outrun it, climb into the crane, and start operating it in a desired manner. (01:18:50)
Plot hole: All pilots have the technology to secretly transmit a code that tells air traffic control there is a hijacking in progress, without having to say a word. They also have a hijack code, something that sounds completely innocuous to you are me, but would be instantly recognisable to the airport authorities.
Plot hole: In one shot before the almost-collision between the C-123 and the Cessna, you see both of the planes on/above a runway. In the next shot, just before the almost-collision, you see the C-123 from behind, with the Cessna in front of it, but this shot is not on that runway anymore, it looks like a taxiway, and there is some airport building in close proximity at the end of it. Nobody would intend to land there (this is before the evasive maneuvre of both). (01:06:05)