Factual error: When Rafe first presents himself at the RAF base, there is a scene with two Spits having the same RF-M squadron designators. Since this was the way individual aircraft were identified, such a thing would never come to pass.
Continuity mistake: During the attack on the smaller airfield where Rafe and Danny are, the photographer who dove in the back of the car gets shot, falls and drops the camera. When it lands it's filming his face, and there is something on the ground right in front of his face, but in the following shot nothing is there.
Continuity mistake: During the attack on Pearl Harbor just after the big explosion we see a captain on the bridge of his ship looking at the attack. The Japanese fire upon the bridge killing many. The captain ducks and goes to the corner, and we see him grab hold of the corner and then release his right hand to his side, but in the following shot his hand is still on the corner.
Continuity mistake: When Rafe is drinking with his friends in the club and Danny is there, Red says, "Maybe we should leave you two alone," then Rafe proceeds to say, "No, no, we're celebrating here." Rafe reaches out to stop Red with his right hand on his chest, but in the following shot it is Rafe's left hand on Red's chest. (Slow-mo may be required.)
Continuity mistake: When Rafe is going in for medical tests and to thank Evelyn her for not taking his wings away, when Rafe starts acting a little strange Evelyn asks "This isn't your chart?" When it cuts to Rafe he is holding onto the IV just underneath the IV bags, but in the following shot his hand is much further down the pole.
Revealing mistake: When the dead nurse's body (Betty I think her name is) is being placed on the pile of dead people, she blinks and twitches her face as the person carrying her puts her down.
Continuity mistake: When Rafe is in the plane trying to get Zeros off his tail he says, "Son of a bitch" and he is very sweaty. In the next shot he's not half as sweaty as the shot before.
Factual error: Towards the end of the film, when the United States launches an attack on the Japanese ammunition factories, the planes fly over Japan and show shots of geishas to establish the country. Japanese geisha communities were shut down by the Japanese government at the beginning of World War II.
Continuity mistake: In the scene where Roosevelt is delivering the "Day of Infamy" speech to Congress watch the microphone placement. The MBC microphone likes to move around from left to right.
Continuity mistake: In the scene where Rafe gets his medical check, he has problems reading. But in a later scene, he has no problem writing letters to Evelyn, and has no problem reading them.
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 Vietnam, and they didn't have helicopter pads on ships until more recently.
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: In the scene showing the bomb on its way down to destroy the USS Arizona, the bomb is a conventional aerial bomb purpose-built for anti-ship use. Historical records state that the Japanese had no armor piercing bombs ready for the attack, so they modified conventional battleship shells with wooden fins instead.
Visible crew/equipment: Ben Affleck's character takes his fiance to the beach in his car. When they are both standing in front of the vehicle, the film crew can be seen in the reflection in the car's bumper.
Continuity mistake: When we see the Navy Department's "vacant sea map", there is a guy holding a cane and explaining what it means. He walks around the globe in the middle of the room holding onto the side of the globe with his left hand, but in the following shot his left hand is on the cane.
Factual error: The scene of Doolittle speaking to the men who have volunteered for what would become the Tokyo Raid is filmed in a hanger. Historically this took place in the crowded Air Ops office at Eglin.
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.