The plane that Tom Cruise and Anthony Edwards jettison from has the same tail markings (i.e. number of the plane) as the plane that Tom Cruise flies later in the movie (i.e. after the original plane crashed.) The Navy assigns each plane its own specific number, after the plane crashes the number does not go back into circulation for a long time.
In the movie there are no numbers on the tails of the F-14's only the squadron markings. The numbers were on the nose of the aircraft. There were two different numbers on the planes. The number on the first F-14 was 104 and the number on the second plane was 114. It may have been the same plane in real life but in the movie they changed the numbers.
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