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 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.