Factual error: The radar guided SAMs are consistently evaded/triggered by the pilots' flares, which in reality only work against heat seeking missiles. Radar guided missiles would be defended against using chaff, basically clouds of aluminium foil strips. It was mentioned in some interviews they didn't want use chaff as it wouldn't really be visible for the audience - hence why they only deploy flares.
Plot hole: Any strike on a military facility by incoming aircraft would first take out the SAM sites with missiles to clear the way for said aircraft to operate freely. After all, the Tomahawks fly right past the attacking planes and take out the runway with no issues at all - no reason they couldn't hit the high and exposed SAMs.
Factual error: The F14 could never have got airborne with such a short clear run unassisted. It needs about 800m, about half a mile.
Deliberate mistake: During the scenes where Maverick is flying the Darkstar spy plane, his helmet is lit up on the inside, so we can see his face. In reality the light would be reflecting off the plexiglass, meaning we would not be able to see his face, and he would not be able to see at all.
Plot hole: Given the mission parameters, why wouldn't the facility be taken out with a barrage of ballistic missiles instead of weapons dropped from manned aircraft? "GPS jamming" wouldn't be a factor with ballistic missiles.
Factual error: When the blue tactical screen is shown, four ships are displayed. Bottom ship is labeled CG-49. CG-49, the USS Vincennes, was a Ticonderoga class guided middle cruiser that was decommissioned in 2005, and scrapped in 2011.
Factual error: The flame coming out of the engine exhaust port on Darkstar when the scram jet is engaged is wrong. That speed at which the burnt gas is being ejected should show the classic supersonic shock diamonds.
Factual error: The pilots are not wearing actual Super Hornet, heads-up display helmets. And, they would not be using clear eye shields in the daytime. Of course, if they were using the sun-tinted shields, you wouldn't be able to see all the acting going on inside those oxygen masks.
Factual error: While flying out, Maverick strikes an object, tearing off his front landing gear. This would have led to a loss of hydraulic fluid, making it impossible to raise or lower his main mounts. It would probably lead to a complete loss of hydraulic fluid to all control surfaces, making it impossible to fly the plane.
Factual error: One of the major plot points is the second aircraft "buddy lasing" so that the bombs will hit the target. Since the target is a non-moving structure, the coordinates would have been programmed into the mission computer onboard the aircraft ahead of time so there would be no reason to have to manually find and aim the laser to guide the bombs.
Factual error: During the steep climb after the bombs are dropped, the max Gs would occur at the initial stages of the pull up. Once the aircraft is maintaining a steep nose high attitude, the Gs should no longer be that high, let alone increasing towards 9-10 G. If they kept pulling that many Gs, they would be flying a loop instead of climbing.
Character mistake: Phoenix says Hangman is the only active-duty pilot in the Navy with a confirmed kill, but she is wrong because Maverick has 3 confirmed kills and is still an active-duty Navy pilot, even though he has been flying test aircraft. (00:25:10)
Other mistake: In the Darkstar takeoff sequence, there is a cockpit shot where Maverick looks back after passing over the Admiral, then looks forward into the cockpit. You can see that the landing gear handle is still in the "down" position and the 3 "gear down and locked" lights are illuminated. At this point in the flight the gear has already been retracted (confirmed visually in the previous external shot).
Other mistake: The film's premise is attacking a target that GPS jamming protects. As the attack starts, it is becomes apparent that no such protection is in place. GPS jamming is a form of radio frequency jamming. It would severely affect all radio communications. But planes and their command carrier are in constant, undeterred radio contact. Moreover, the enemy uses radar-guided SA-3 Goa SAM units that would have been unable to operate properly in jamming conditions.