The payloads the fighters carry changes between shots, from nothing, to only missiles to missiles with drop tanks.
The machine gun fires repeatedly even though no ammunition can be seen to be going into it, then as the shot changes sometimes it has a belt of ammunition.
The "bmps'' are loaded into the transport facing forwards (although the turret is facing backwards). However, when they exit the crashed transport, they exit moving forward when they should have been backing out.
During the assault on the missile base, Cooper declares that he has but one Maverick missile left, yet in the next shot (which is an outside view of his aircraft and his wingman's), he quite obviously still has 2.
The Soviet aircraft are referred to as Mig-29s, yet they are actually F4 Phantom II's.
The Soviet BMP-5s are actually M113 armored personnel carriers with a mock turret and missile rack added on.
The F-4 Phantom II fighter-bomber was shown as a single seat aircraft. F-4 Phantoms are two seat aircraft with the radar operator sitting behind the pilot. Therefore when the Russians landed in Israel for the mission, 4 officers should have climbed down from the aircraft instead of just 2.
The "Mig 23's" fought are actually F-21 Kfir C7 produced by Israel (in fact in the first movie they simply switched the color scheme on them). However, the Israeli Air Force has a long history of assisting in films involving air combat. This isn't a "goof" so much as a practical substitution issue.
On 2 occasions, a Sidewinder missile is fired at ground installations from the wingtip of the F-16 aircraft. Sidewinder missiles were not designed to hit ground targets and while they might be able to, they would like as not fail. Also, shots shown after these missiles had been fired show that they are back in place.
In the widescreen format of the movie, shown at the cinemas in Bulgaria in September 1991, a hand of a crew member, moving slowly the B-52 model in front of the camera, was clearly visible.
When Cooper was laying in bed after he was grounded, Bush approached him and saluted him. This is wrong. Bush is a Major and Cooper is a Captain, meaning Bush outranks Cooper, so it should be Cooper saluting Bush. In addition, they were indoors where saluting is prohibited and neither one was standing at the position of attention.