Continuity mistake: In the scene where Goose is in the bunker with everyone else, he says "Planes. Should we fire?" When he says this, we see him staring down the site of a 50 cal. In the next shot, we see the gun, but no Goose. And we know it's the same gun, because Red was by it both shots. Yet when we see the gun in the very next shot he is holding it again. He had no time to move away and back to the weapon again.
Visible crew/equipment: During the scene where Danny and Rafe are being chased at low level by several Zero fighters, there is one camera shot where we can see past a P-40's tail at the Japanese attackers. The nearest Zero appears to have a strange object attached to the top of its fuselage, just in front of the tail. Presumably, this object is a remote-controlled camera which was used by the film-makers for the aerial combat scenes.
Continuity mistake: In the scene where the Red head boy is proposing to the nurse, 2 men walk by together, one wearing a light coloured shirt with some scattered pattern on it, and the other wearing a plain white shirt. Then they walk by again a few seconds later.
Factual error: All of Jimmy Doolittle's "raiders" had leather flight jackets prepared especially for their mission to bomb Tokyo. On the back of the jackets was a message written in large Chinese characters that explained who they were so the Chinese (if the crew were lucky enough to reach unoccupied China which was the original plan) would not kill them. I also believe there were large U.S. flags and Chinese flags (the old Republic of China style) painted or sewn on the back of these jackets as well. This important costume detail was omitted in the movie.
Revealing mistake: When Betty's body is being placed amongst those killed outside the hospital, the dead guy lying on the left side breathes at the wrong time (you can see his neck and head move slightly). (02:01:55)
Continuity mistake: When Rafe meets Evelyn outside the hospital with a bottle of wine, he accidentally hits his nose with the cork and lays his head on Evelyn's lap. Her right hand is holding some ice, but her left hand is nowhere to be seen, but in the following shot her left hand has appeared on Rafe's chin and cheek. (00:17:40)The-Immortal
Continuity mistake: During the attack on Pearl Harbor, Rafe, along with a couple of other pilots jump into a convertible car to drive to another airfield. The actual set they depart from (which is exploding all around them) is the same one they "arrive" at minutes later, but the whole set is intact, instead of an actual different set/location.
Continuity mistake: When Red and his army friend pull up next to the four nurses at the side of the road, Red asks Betty if she wants to come for a ride. Red leans forward and puts his hand on the steering wheel, but in the following shot he is leaning back with his elbow on the top of the door. (00:42:30)The-Immortal
Continuity mistake: Just after the Japanese attack and the shot cuts to the airfield where they all are gearing up to fight them in the air, there is a shot of two guys on a roof of a building that are shooting the Japanese planes. They get shot and fall down, but in the following shot you can see they have come back to life. (01:31:35)The-Immortal
Factual error: In the scene where the Japanese aircraft are launching for the attack on Pearl, an officer on one of the carriers holds a white flag in his right hand just as the planes are about to take off. Look carefully; the wind is blowing from the stern of the ship towards the bow (as evidenced by the position of the aircraft in the background). The flag should be moving in the opposite direction, as the carrier would be turned into the wind and moving forward at top speed to launch aircraft.
Plot hole: Danny receives the telegram from Rafe, telling him that he is alive, at the same time Rafe meets with Evelyn. The telegram must have been sent from Hawaii. Why didn't he just call on the phone? When Rafe reached the U.S. after leaving England why didn't he send a telegram then. In those days it took some time to travel from the Eastern U.S. all the way to Hawaii and there is no way he beat the telegram if it was sent when he returned to the U.S.
Continuity mistake: In the middle of the film just after the Japanese start attacking Pearl Harbor, Cuba Gooding Jr sees the captain injured. If you watch closely, the captain is pointing at Cuba but doesn't touch his arm, yet in some shots you can see that his hand is touching his arm. (01:30:05)The-Immortal
Continuity mistake: In the scene where Danny, Rafe and Jimmy Doolittle are on the deck of the Hornet talking about "returning" the friendship medals before the attack on Tokyo, you can see what appears to be a radar dish covered with a grey tarpaulin. The scene cuts back to Doolittle, Danny and Rafe talking some more, and then back to a wide shot of Doolittle walking away. The mysterious tarped object is completely gone now.
Continuity mistake: When Rafe and Evelyn go to the Queen Mary ship and they are rising on the platform, and kissing, one sweeping camera shot shows the handle of the elevator controls going straight up. This would mean that they had stopped, yet they are still moving up. A couple of seconds later, a close up of the handle shows that it is now in the position to move the elevator up.
Plot hole: In the scene where Danny and Evelyn are talking, Danny 'finds out' that Rafe volunteered to go to England. Danny already knew that Rafe volunteered because near the start of the film, Danny was in the same office as Rafe when Rafe was given the choice to go to England or not.