Plot hole: Near the end of the Tokyo raid, Col. Doolittle orders his radio operator to "break radio silence" so he can address the rest of the planes. For the duration of the raid, though, intelligence officers had been listening to radio transmissions back at Pearl (other users have already commented that this in itself is a historical error). If these transmissions were being heard at Pearl, there was obviously no radio silence to begin with.
Continuity mistake: When the cook uses the mounted gun it has two ammo cases and then during the scene it changes between one and two cases and the right hand one is even open at one stage. (01:36:40 - 01:37:15)
Continuity mistake: When Rafe comes back for the first time after supposedly being dead and you see his reflection in the glass before meeting his lover, as the camera pans across the room you can see a green light moving on the wall as the camera moves. I'm not sure what it is but it could be the light to indicate the camera is on.
Continuity mistake: When Danny & Rafe take off from the sattellite airfield their landing gear is (obviously) down. You see a shot of them from behind like this. Two seconds later they just clear a building, in the heat of a combat takeoff,and both sets of landing gear are fully retracted.
Continuity mistake: After Rafe hits himself with the cork, Evelyn puts snow on it. She then is seen removing it, but when the camera angle changes, the snow is back on his nose.
Continuity mistake: When Evelyn and Danny are having a drink in a cafe going over the good times with Rafe, we see the camera pan down from a height, in this shot we see Danny holding onto a cup in his right hand which is sitting on a saucer on the table, but in the following shot he is just putting it down on the table. (00:52:45)
Other mistake: During take off from the carrier, 600 miles at sea, trees and a shoreline are in the distance.
Continuity mistake: When Rafe's girlfriend is looking for him at the train station there's a train behind her that says "Silver Horizon." But when the camera shows Rafe looking at his girlfriend the words on the train are gone.
Factual error: Early in the film, a close-up of Rafe in his Army Air Corps uniform shows his wings. The wings are not Army Air Corps, but the "shield and stripes" of the US Air Force, which did not exist at that time. Additionally, when a priest is giving last rites to the dying, he says, "In the name of the Father, the Son and the Holy Spirit." But before the Second Vatican Council, it was "Holy Ghost."
Factual error: In the shot where they show the pictures the Japanese spies took, you can see the helicopter pads on the ships. Also, during the attack, helicopter pads are visible on some ships. The helicopter was not used until the Korean War, and they didn't have helicopter pads on ships until more recently.
Factual error: While the hospital did sustain some damage during the actual battle at Pearl Harbor, the Japanese forces did not deliberately target or fire upon it. Hospitals are usually avoided in battles as the people within are not in any condition to fight back and it would just be consuming ammunition that would be needed for attacking more practical targets such as enemy aircraft, assault vehicles, weapon repositories, and such.
Factual error: The USS Hornet, a Yorktown-class aircraft carrier launched in 1940, is played by a much more modern Kitty Hawk-class carrier. The B-25s also take off from a steel deck instead of a historically accurate wooden deck.
Factual error: As the RAF aircrew are running for their aircraft during the scramble sequence, one of the Spitfires can be seen showing a serial of 'AR4474' briefly. This is incorrect not only for a wartime Spitfire, but is completely out of sequence for any UK military aircraft. All four flying Spitfires used during filming had similar inaccurate serials. (00:38:20)