Sam Axe is a Navy Seal, but is not wearing a Special Warfare pin above his left pocket. Instead he has a surface warfare pin and on the pocket cover, a BUDs device (Basic Underwater Demolition). Even though he could have been previously qualified as a surface warfare officer, he would have worn the Seal pin instead.
While Sam and Michael are drinking beer in the café, we see that Michael's glass is almost completely full when he decides to leave, just a couple of (movie) seconds later he turns around towards Sam and we see that the glass is about half full.
When the helicopters come up firing, you can see the actors' breaths and see fog in the background scenery. Just prior to and following the helicopters' arrival and firing, the sun is shining and no frigid temps.
Naval Officers do not wear black shoes with the white uniform the shoes should be white. As a commander his cover (hat) should have "scrambled eggs" on the visor. The shoulder boards were not properly attached. While
the are times when it is proper to salute indoors, Naval personnel
never salute without being covered (wearing the hat).
Several uniform mistakes for Sam: Sam is called a Navy SEAL but in the beginning is shown with a surface warfare officer breast insignia instead of a special warfare insignia. Ribbons in the Navy are worn such that rows are touching each other, but Sam wears them with a space between rows. None of his ribbons are ribbons that I have seen, and he has an extremely small number of them for an O-5 (CMDR) especially a SEAL O-5. He is also missing a ribbon that all members of the armed forces would have in 2005, the national defense service ribbon.
A "military court" would not have issued a ruling (as stated in the voice-over during the airport scene) without a formal proceeding. The question and answer session was not a formal military proceeding, even though a female character appeared as though she was supposed to be transcribing the session.
If Sam was asked to wear dress whites to the board, then the officers on the board would also be wearing dress whites. If Sam was asked to wear summer whites to the board, then the officers on the board would also be wearing summer whites. Instead, Sam says he was asked to wear dress whites, and he wears summer whites, and the officers on the board are wearing khaki. Also, if it was a true board of inquiry, there would have been at least three officers on the board, but in this case only two officers were present.
Right at the beginning, Sam is wearing "whites", with the shoulder boards of a Commander in the US Navy (O-5). However, his cover (hat) does not have the "scrambled eggs" on the bill as is regulation for O-5 and higher.