The film takes place in 1962, but the aircraft are F-4J Phantom II's, an aircraft that was manufactured in 1966. The aircraft have ECM antennas on the intake shoulders, which were added in 1975. Finally, the planes are gull-gray on the bellies and noses. This was a paint scheme mandated in 1978.
During the last scene of Bull Meechum with his family on the porch prior to the Prom the youngest son is wearing a jacket covered in aviation patches. One of these patches is for the F-14 Tomcat which first flew in 1970 and wasn't operationally deployed until 1974. The film is set in 1962.
When Santini and his oldest son are at, what appears to be the officers club, there is a full shot showing Santini standing to make a toast. On the table there is a bottle. In the next full shot, the bottle has moved about four inches to the viewer's left.
Bull Meechum meets his old buddy, Virgil Hedgepath, and they wrestle each other in Hedgepath's office. In the background, you can see a couch. As Hedgepath gets Meechum in an arm lock, on the floor, you can see that the floor has been raised: in the background, the couch is noticeably higher, and you can see the side of the platform that the actors are on, directly below Robert Duvall's face. Filmed in a 4:3 ratio, the raised floor was cropped out for the 1:85 theatrical release.
The squadron that Bull Meechum assumes command of, VMFA-312, was known as "Checkerboards", not "Werewolves". In the opening scene, he dogfights with two navy F-4s while flying a VMFA-312 jet. Supposedly, he left that squadron in Spain! Also, the tail letters for VMFA-312 are "DR", not "DF".
In Colonel Hedgepath's office, he admonished, "And don't go attacking anymore corporals on the latrine!" No Marine would refer to a bathroom as a "latrine"; that is an Army term. In the Marine Corps and the Navy, the term is "head."
In the opening dogfight sequence you hear the lead pilot call
"Okay, it's Marines verses Navy"; and you see a F-4J Phantom with the word Navy on the side. However, the squadron designation is VMFA-251. At the time, only Marine Phantoms carried the "VMFA" designation, Navy Phantoms were "VF" . The "Marine" squadron was in fact VMFA-251 Thunderbolts, who now fly the F/A-18C.