In this game, we're told that Para-Medic, the female doctor from Metal Gear Solid 3: Snake Eater, was Dr. Clark, who Naomi mentioned several times in Metal Gear Solid. However, Naomi always referred to this person as male. This is an unfortunate translation error: the Japanese language provides many gender-neutral terms, so Clark's gender was never specified in the Japanese version of the first game. The "Metal Gear Solid Database" which Konami has released retcons this by claiming Dr. Clark was secretive, and Naomi mistakenly assumed she was male as a result.
Mei Ling wears an male officer's hat, whereas she should wear a female version.
Mei Ling is wearing a service uniform on a ship, whereas it would be more proper to wear a working one. However, given that the ship in question is a training vessel abandoning the chain of command to launch a paramilitary action during an international crisis, this was likely not possible and would have been a comparatively small lapse in protocol.
Mei Ling, when introduced as a Navy Captain, is wearing a uniform called (Navy) Winter Blues. This particular uniform was phased out by 31 December 2010. If the game takes place in 2014, the wear of this uniform is improper, especially by a senior officer. However the game was published in 2008, and the phase-out date and corresponding grace periods were not well-defined then. The depiction in the game is as accurate as was possible at the time.
During its engagement, the Missouri crew are seen running the ship from its vulnerable bridge. Iowa-class battleships such as this have a heavily-armored conning tower that acts as the command center during combat.
Big Boss mentions to Snake that Snake killed him twice before, this is incorrect, Snake did kill Big Boss during the events of Metal Gear 2, but during the events of Metal Gear, the "Big Boss" that was killed was in reality Venom Snake his Double.