Although the film opens with a title that says 1944, the song being played at the U.S. base is "It's Been a Long, Long Time," which was written by Jule Styne and Sammy Cahn to celebrate the war's end and not released until 1945.
During the initial bombing run to Berlin, one of the bomber pilots says that engine number three is losing pressure, but when the shot goes to the plane's exterior, engine number one has stopped operating.
When Joe 'Lightning' Little is being reprimanded by Colonel A.J. Bullard in his office, Joe is wearing his headgear. But when he steps out of the office he is no longer wearing it. This is backwards. Army regulations state that when a soldier is outdoors, he is supposed to have his headgear on. He is then supposed to remove his headgear as soon as he steps indoors.
The Germans are often seen utilizing 20mm antiaircraft guns against the Tuskeegee airmen at low altitude, with near misses resulting in characteristic puffs of dark smoke near the planes. These puffs of smoke in reality only originated from timed fuses that were only used in heavy antiaircraft artillery, such as the 88mm. A 20mm shell would have simply whizzed by the plane and exploded upon contact with a hard surface, rather than exploding as it came near.
When the pilots attack the German Navy vessel, it is referred to as a "destroyer". However, the close ups of the attack reveal the vessel has multiple 8-12 inch guns in armored turrets, which would make it at least a cruiser and maybe even a light battleship.
In the opening scene, the German flight leader is not wearing his oxygen mask throughout the entire battle. B-17 missions were routinely at altitudes of 25,000 feet (all the American characters are wearing masks). Without the oxygen mask, the German commander would have passed out in a matter of minutes.
Whenever P-51 Mustangs are shown in flight, they are accompanied by their trademark gun port whistle, even while in level flight. In actuality, the whistle only occurs during high G turns and climbs, when the angle of attack on the gun ports is sufficient to create the sound. Some attribute this noise to the supercharger on the Rolls engine, however in fact it is created by the gun ports, and as such demilitarized P-51s with their gun ports removed do not make the sound.
When the Tuskegee Airmen perform their first mission in P-51 Mustangs, several of the planes are heard starting with the trademark inertia starter squeal of a radial piston engine. However, the P-51 always used a water cooled V12 engine (both early Allison and later Rolls) which have a conventional starter and turn over with a noise similar to any modern piston aircraft engine.
At the end of the briefing, all the officers stand up and salute the commander as he leaves. This is not correct military protocol. They would have only stood at attention as the CO enter or leaves the room unless doing so takes the lower ranking member away from their duties. You only salute a superior officer if you are reporting directly to him.
Immediately after the hearing in Washington (at around 19 mins), the high shot of the camp shows a P-40 with its insignia on the top of the right wing. US military aircraft have their wing insignia on the top of the left wing and underside of the right wing.
P-51s of the time were bright silver in appearance due to their unpainted aluminum finish. The P-51s in the film are obviously painted silver. (This is quite understandable, as the aircraft used for filming all came with different finishes and had to be repainted.)
The goof item below may give away important plot points.
During the final battle Joe 'Lightning' Little goes head to head with an ME-262 in which he is wounded by the enemy fighter's guns. In reality, the ME-262 was equipped with 4 × 30 mm MK 108 cannons which are exploding rounds and would have killed him and obliterated his P-51 on impact.