Other mistake: In the scene in which two Japanese Zero fighters bomb and strafe a PT base, shots of the attacking planes show them carrying no bombs. During the attack, they still drop around 20 bombs anyway, which is considerably more than the actual carrying capacity of the two planes.
Continuity mistake: When PT 109 crashes into the hut at the end of the wharf it is doing about three knots. The shot before (across the stern) shows the wake of a boat doing about 35 knots. When the boat actually hits, a sailor falls over, the wrong way for someone caught by inertia and at the same time, on the port stern bollard, you can see a line fastened and leading ashore. The boat is supposed to be moving alongside the wharf off to starboard: (a) there is nowhere for that line to be fastened to, and (b) the boat is supposed to be still underway.
Factual error: Prior to the shakedown cruise as the base is being strafed and bombed by the Japanese planes, the twin engine plane in the scene (perhaps meant to depict a Kawasaki KI45) is a 50's vintage Piper PA-23.
Factual error: All of the PT boats in this film are painted in the same Navy Gray used by larger warships of the US Navy in WWII. However, the real PT 109 and the other PTs in its squadron were painted green in order to better blend into their daytime anchorages or moorings near island jungles. The common green color scheme of this period was designated as "Design 5P" and incorporated Navy Green over a base coat of Ocean Green.
Other mistake: When JFK meets with Australian coast watcher Evans, he tells Evans he only has three shots in his revolver. Evans gives him his rifle for the fourth recognition shot. That revolver should have held at least 5 to 6 shots. When did JFK fire the others? We never see that prior to that scene.