When Maverick leaves Charlie's house after he has dinner with her, there is a For Rent sign in her yard (as there is when he drives by her house later in the movie), but there wasn't one when he arrived.
During the final dog fight, Iceman's F-14 is hit, resulting in him shutting down an engine. This is now an emergency aircraft needing priority handling and landing ASAP. However, upon returning, Iceman elects to do a single engine high speed flyby with Maverick.
Exactly where Hop 31 takes place is totally inconsistent. When Maverick is in the flat spin he is above a rocky, desert area, yet somehow crash lands in the ocean nowhere near any desert terrain.
In the stairwell, Iceman puts on a watch twice.
In the mission when Maverick has Sundown as his RIO, Jester's plane alternates between a plain gray paint job, and a camoflauge one.
In the final engagement when Maverick says he is "supersonic," the next shot shows his F-14 with the wings in the extended position. For an F-14 to be traveling at supersonic speeds, the wings would have to in the swept back position. He could not have forgotten to sweep his wings back because the wing geometry of the F-14 is not pilot-controlled; it is controlled automatically by the flight computer.
There are several scenes of Maverick walking outdoors without a cap or hat; in the Navy and Marines, this absolutely is not done.
The center of the story at the pilot training school is a series of competitions that lead to the awarding of the "Top Gun" trophy. The real flight school has never had that trophy or anything like it, as the training is designed to encourage cooperation amongst the pilots.
In the opening, a full-screen explanation of the Top Gun program says it was created "to "insure" that pilots receive the training..." etc. The correct word in this case is "ensure" as in 'to guarantee.'
During both the training missions and dogfight scenes, the sound effects for the targeting system and the radar/missile warning are nearly identical. In reality, those two sounds would be completely different so as to give the pilot no doubt as to what's going on (as evidenced when Maverick appears confused when he hears a "lock on" tone when Jester "kills" him while Maverick's chasing Viper).
Navy rules state on tactical jets, oxygen shall be worn from takeoff until landing, a rule broken throughout the movie. Real Navy/Marine Corps pilots break this rule all the time as well.
Flight crews are seen throughout the film wearing golf shirts under their flight suits. While it is more common to wear a t-shirt under the flight suit, in the 1980's up until the early 2000's, crews did have the option to wear a golf shirt with their squadron colors under their flight suits.
When Charlie chases down Maverick on his motorcycle her car has a blue DOD decal on its windshield. Blue decals are used for officers, red decals for enlisted. As a civilian employee she would have had a green DOD decal for her car. The vehicle "Charlie" is driving was borrowed from her "older date" at the beginning of the movie hence the vehicle having a blue DOD decal.
Goose is depicted as a Lt (jg) and wears the proper insignia: on a white uniform, shoulder boards with one thick gold bar and one thin, and in khakis, a single silver bar (a full lieutenant wears double silver bars). (Some thought he was wearing full lieutenant insignia; they are similar.)
The insignia for a Navy Lieutenant happen to be the same as for Army and Air Force Captains. Thus, Maverick and Iceman are correctly wearing Lieutenant insignia.
Maverick fires the same missile from the same wing station at least three times. This is because only two live missile launches were authorized by the military and so the footage is repeated many times throughout the film along with model shots.
During the first hop, Jester states that the hard deck would be 10,000 feet. However, during most of the engagement, it can be seen that the fighters are flying much closer to the ground than 10,000 feet. They fly through the terrain, and at one point Goose even says "Watch the mountain!" Since the tallest mountain in San Diego County doesn't rise above 6,600 feet, there would be no way for them to be in any danger if they were actually above the hard deck.
When Maverick and Goose get in trouble for flying by the tower, there is a closeup of Jester's flight suit. His pilot's wings are for a USAF Senior pilot, not a Naval Aviator's wings.
Several times missiles that are supposed to be live for combat can be seen hanging from aircraft wings. The missiles have a blue band around them indicating they are inert training missiles. Live missiles would have a yellow band as a warning of the live high explosive warhead.
In the elevator scene, Charlie's hair is noticeably darker than in other scenes. This is because this scene was shot after principal photography, and Kelly McGillis had already dyed her hair for another film role. The filmmakers tried to hide her darkened hair with the cap, but it's still noticeable.
When the command deck officer informs Stinger that the catapults are broken and that they can't launch aircraft, the officer's lip movements don't match what he says.
(at around 1h 27m) When Stinger says "The communication ship SS Layton has become disabled and has wandered into foreign territory...", the movement of his lips doesn't match what he is saying.
When Maverick is driving his motorcycle along the runway with the planes taking off, the bed of the truck he's atop of can be seen at the bottom of the screen.
At many points during the briefing prior to the first hop, men can be seen reflected in the actors' glasses, presumably crew members. They can't be characters, as Charlie is the only one standing in front of the men at this time.
During the recovery of Goose and Maverick, the safety cable attached to [link-nm0000129] can be seen.
(at around 48m) When Maverick steps into the elevator, a crew member can be seen reflected on the picture frame on the wall behind him.
For the first hop, the hard deck, which is the simulated ground level, is set at ten thousand feet (nearly two miles), meaning that for the pretended combat, there would be a buffer from the real ground. It is assumed that this is ten thousand above ground level, but when the pilots fly the hop and shoot Jester down, there are mountains very close, and Goose even warns Maverick to watch the mountains, as he nearly crashes into them.
The final dogfight happens over water, yet a mountain is visible in the corner of one shot.
At the beginning, they are in the Indian Ocean, but during one of the fight scenes, mountains can be seen in the background.
A rescue mission would not send out only two Tomcats (i.e., Iceman and Hollywood who was replaced by Maverick after he was shot down). A 1980s US Navy Air Wing had two F-14 squadrons, two attack squadrons of A-7s or new F/A-18s, two all-weather attack squadrons of A-6s, E-2Cs for Early Warning and other support squadrons. They clearly couldn't secure filming these and the focus was on Maverick.
The term "bogey" is misused throughout the movie. A bogey is an unidentified aircraft. Once identified, it is referred to as a "friendly" (for friendly aircraft), "bandit" (for non-friendly aircraft) or "hostile" (for non-friendly aircraft that may be fired at). In USN terminology, a non-friendly surface radar contact is a "skunk".
During the final dogfight, Slider tells Iceman that there is a MiG "on your left, 3 o'clock." The 3 o'clock direction is to the right; 9 o'clock would be the left.
When Maverick and Charlie are having dinner, Otis Redding's "(Sittin' On) The Dock of the Bay" comes on and Maverick remembers his "folks loved it", then states his father "disappeared in an F-4 November 5th, 1965," yet this song was not written until November 1967.
In the flat spin sequence, Goose calls "Altitude 8,000, 7,000, 6,000", but when he calls "6,000" the altimeter is passing through 2,000 feet.
During Cougar and Merlin's approach to the carrier, the approach controller makes a call to their aircraft, "Cougar, you are well below glide path at 3 quarters of a mile. Call the ball." Then, the Landing Signal Officer hears a reply, "Roger, ball," without ever hearing Cougar confirm that he had the ball in sight. Additionally, the approach controller made radio calls to both Maverick and Cougar, referring to both of them by their call signs, which is something never done over the radio. Anyone calling their aircraft over the radio would refer to the aircraft's mission call sign, in this case, "Ghostrider 117" for Cougar and Merlin, and "Ghostrider 203", for Maverick and Goose. Once the approach controller tells the approaching aircraft to "call the ball", Maverick's reply, for example, should have been "Ghostrider 203, Tomcat ball, 1 point 1." That lets everyone know several important pieces of information. One, the aircraft call sign and type of aircraft approaching, so the sailors working the carrier arresting gear know the proper tension to set on the wires for a safe landing. Two, the fact that the pilot sees the ball, so that the LSO can take over control, and guide the crew down to a safe landing. Three, the amount of fuel the aircraft has remaining; in this example 1,100 pounds of gas remaining. That way, the LSO knows how to properly sort the approaching aircraft by amount of fuel remaining, should the aircraft miss the wires, and be forced to make another landing attempt, divert to a land base, or join on the tanker for more fuel.