Revealing mistake: When the Japanese planes fly over the hill towards the harbor to bomb it, you can see a cross on the hill. That cross was not there back in 1941 during the raid. It was put there afterwards as a memorial to the point where the enemy planes first came over the hill.
Revealing mistake: During the scene in which the Japanese are planning the attack, one shot has several of the Japanese Officers looking at aerial photographs of the harbor. These pictures appear to be attached to some sort of poster board and on the back of one of them is the "Recycled Paper" emblem (the three arrows bent back on each other). Visible on the DVD.
Revealing mistake: Other users have commented on the placement of the island on the Japanese carriers. If you watch the launch scene very carefully (as one squadron of planes flies over another of the carriers), the carrier is a modern, angled deck carrier, but the planes are all lined up backwards. As the shot moves over the ship, you can plainly see the bow of the carrier (with the protrusions for the catapult water brakes, and Japanese planes lined up on the bow, facing the stern). As the shot progresses down the ship, you will see the angled deck amidships, with the island where it belongs, and the planes taking off over the stern.
Revealing mistake: After Danny's plane crash lands in China, and Rafe runs towards the crash site, he shoots a Japanese soldier. After his next to last shot, the slide locks back on his pistol, indicating it is empty. You can see the slide locked back moments before he takes his last shot, with an empty gun.