2. Not Shooting Gordon When They Captured Him - Half-Life
One of the all time dumbest moments in video game history has to be the Marines' capturing of scientist-turned-badass Gordon Freeman halfway through the brilliant Half-Life. So, when they have him, what do they do? They throw him into a trash compactor of course, because there's no possible means of escape, right? Well, Gordon escapes and subsequently manages to complete his quest, of travelling to Xen and defeating the Nihilanth, and living to fight another day, something which could so easily have been avoided had the HECU soldiers just popped a bullet in his head. It's gross incompetence on a massive scale. Given that the HECU officers had orders to kill any civilians they found in order to cover up the Black Mesa incident, dumping him with the trash is a Bond villain-esque folly of epic proportions. It could have been over so easily.