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.