Plot hole: The admiral receives the news of the stolen aircraft from the general over an open radio, with umpteen enlisted personnel within earshot. However, when the air group commander asks what the OP is about, the admiral tells him that it is on a need-to-know basis.
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Mistakes
At 0500PST the CAG suggests to the Admiral that they should take the plane out with an airstrike, because once it is airborne they won't be able to find it. However, it is not until four hours later that the CAG is actually briefed on the mission. How does he know the target before the briefing? See more...
Flight of Fury mistakes
Factual error: A SEAL team is sent in to Afghanistan; first they're referred to as "SEAL team Baker One", then a moment later they're "Ranger team Baker One". There's no part of that that isn't wrong. To make matters worse, the gear, weaponry and tactics they use are all wrong too as well as a single team being dispatched highly unlikely.
Plot hole: In order to attempt to recover a secret aircraft, Steven Seagal's character is instructed to abandon his own plane, a super-secret SR-71 Blackbird, at an airfield in Afghanistan.