The F-16 that Mitchell uses for the final dogfight has empty wings and missile rails in the first air to air shot after he takes off, but has a full load for the rest of the sequence. Also, it is a two-seat variant.
The stolen stealth plane in the hanger scenes looks different to the one in the flying sequences.
When chasing down the F-117 with the F-16, the scene where he catches up actually shows two F-117s, not an F-117 and an F-16.
There are no colonels in the US Navy.
The military is not going to allow a service member, especially a pilot, to wear a pony-tail on active duty.
GPS receivers do not transmit any signal and could not be used as a tracking device.
The stealth plane is shown using air to air missiles, which were never fitted to this type.
Ice-T tells the crew to load a total of five missiles. The F-117 only held two. I did not catch the model of the two nuclear missiles, but it certainly could not be equipped with three AGM-65s.
When Mitchell commandeers the F-16, his canopy doesn't close
all the way.
The CAG then later shown as the Admiral wears submarine officer's dolphins and the capt. of the Normandy wears pilots wings. Also, another officer on the submarine wears Surface Warfare Officer insignia.