The scene that shows the Japanese planes attacking the hospital caused a great uproar, both in Japan and among Pearl Harbor veterans, because this never happened. The Japanese pilots were under strict orders not to attack civilian targets. Survivors note that even when the Japanese had a straight line of attack, they never attacked the hospital itself. This wasn't purely for humanitarian reasons: ammunition was typically saved for tactical targets such as ships, aircraft and weapon repositories. Director Michael Bay said he added the scene to make the attack seem more barbaric.
When shooting the scene where Rafe (Ben Affleck) and Danny (Josh Hartnett) manage to get off the ground during the attack, and are chased by three Japanese Zeroes, one of the real planes clipped a palm tree and crashed. The pilot was dazed, and suffered only a broken finger.
The character portrayed by Cuba Gooding Jr., Doris "Dorie" Miller, was the first black man to be awarded the Navy Cross. He was later assigned to the escort carrier Liscome Bay. Miller was reported missing in action in November 1943, when it was torpedoed during the Battle of Makin Island.
Jon Voight wore duplicates of the steel leg-braces that President Franklin D. Roosevelt had to wear. As a result, Voight suffered from bruising and chafing on his legs for weeks after finishing his work for the film.
For the scenes of the Japanese planes taking off, an American carrier was used. According to Michael Bay, this greatly offended some of the Pearl Harbor survivors, who felt it dishonored the dead. Bay, however, pointed out to them that they destroyed all of the Japanese carriers later in the war, so an American carrier had to be used. He says that when he pointed this out, they agreed to the use of the American carrier.