When Flight 117 is commanded to "pull up" in order to avoid hitting the other aircraft on the intersecting runway, the pilot decreases the throttle sharply from the maximum power position. In reality, a plane in descent would have the power level at an extremely low position, and 117's pilot should have applied throttle.
When Masters (Nick Chinlund) is shot by Jack and Renée, there is fake blood visible on his hands before his body gets riddled with bullets and he has a chance to touch one wound.
One of the air traffic controllers says that he can hear the pilots talking to Almeida. There is no way that he could know that name because the F.B.I. didn't tell them who was behind this.
Towards the end agent Walker stares at a notebook computer deleting its files instead of quickly pulling the plug and/or battery.
When the air traffic control supervisor takes the call from Tony, he turns and tells a subordinate to call the FBI to have the call traced and then hangs up in less than 10 seconds. No where near enough time to complete a trace.