When setting the sail early in the movie, Power's character refers to a halyard as a sheet. No real sailor would make such an error.
When the Japanese navel vessel appears it is displaying the Hinomaru which is the national flag of Japan, however during the second world war both the Japanese army and Navy had their own respective flags.
Ensign Palmer said the navy rank of Ensign was equal to an army Major. This is not true since an Ensign is pay grade O-1 and Major is pay grade O-4. An Ensign would be equal to an Army Second Lieutenant.
In several scenes, but especially the firefight in the church, many of the Japanese soldiers are carrying .30 caliber Springfield 1903 and M1917 Enfields - both standard U.S. Army issue in WWI and the early days of WWII. While it could be that the Japanese were using captured equipment, it would not make logistical sense to carry rifles with a different caliber then their standard issue 6.5 mm Arisaka Type 38 rifles.
Early in the film, Ensign Palmer is told by Juan Martinez that there are no boats with engines available and so the crew buy a sailing boat to try and reach Australia. Later in the film however they agree to try and get a message through to the American General and in return he will arrange for them to be sent to Australia.
However when trying to reach him, they steal a Japanese boat which has an engine but instead of using this to go DIRECTLY to Australia they carry on trying to reach the General for him to help them get there.