Stupidity: No U-boat commander is going to "finish off" a ship that is dead in the water and is on fire from stem to stern. He exposes his boat and his men to mortal peril by surfacing, brightly lit by a full moon and the fires burning on the sinking ship, making them a sitting duck for the destroyers that might well be still in the area. He also wastes a precious torpedo for absolutely no net gain.
Stupidity: Given Laurie Strode survived an attack by a still on the loose maniac she's not guarded at the hospital?
Stupidity: When the crew of the German U-boat boards Katanga's ship, the submarine moves in a position perpendicular to the ship's bow as if to block its path. In reality, this would have been a pretty stupid move by the German captain, as Katanga could have rammed the submarine easily. Any kind of damage to the hull, especially ramming damage (even from small ships), would have been catastrophic to the submarine. It makes no sense to make a manoeuvre like this.
Stupidity: When the shuttle arrives with the assassins, O'Niel is shown loading a shotgun, then he carries that gun when he runs to his office. When he leaves his office again to confront the assassins he grabs another shotgun from the locker. Why didn't he just grab the gun he walked in with?
Stupidity: When the duke approaches the wall at the end, Snake dives on him and briefly knocks him out. Snake could have easily grabbed his gun back and left the duke unarmed (or even just killed the duke there and then), but just gets up and runs, leaving it with him.