Factual error: Before departure, Captain McNeely asks if the ship's mission has anything to do with the Manhattan Project. The Manhattan Project was highly classified, and it is doubtful that McNeely had heard the project's name. In fact, there is historical debate as to whether or not he knew what the cargo was that he was carrying.
Factual error: McVay gives the order to cease zigzagging, full speed ahead, but the Japanese sub commander gives the target speed of 12 knots for the torpedo solution. The Indianapolis was capable of a speed in excess of 30 knots.
Factual error: In the movie theatre, you can hear the voices of Larry and Shemp in The Three Stooges short "Brideless Groom." The events in the movies are from July/August of 1945, but Brideless Groom was released on September 11, 1947. Also, the Three Stooges were still Moe, Larry, and Curly in 1945, Shemp did not start filming with them until 1947. (01:09:10)
Other mistake: During one of the shark attacks, water is falling on the ocean suggesting a rain shower, while overhead there is nothing but clear blue sky.
Other mistake: Sloppy animation: In the opening scene, the propeller of one of the Japanese planes stops just as it rolls into its dive.