3. Star Wars Episode I: The Phantom Menace
The Plot: Qi-Gong Jin is told that Anakin is too old to take on as an apprentice, that he may become dangerous in the future. Qi-Gong in his infinite wisdom tells his other apprentice Obi-Won to train Anakin anyway. Anakin turns into Darth Vader, and helps orchestrate a plot by the film's real villain, Darth Sidious, to take over the galaxy. Nice job breaking it, Qi-Gong.
The Solution: Listen to protocol. How hard is it, really, just to follow the rules? I know the Jedi have some pretty strict laws and all, but how hard is it to just take a "no"? I don't care if he's Force Jesus. If your superior, the 900 year old puppet, tells you that it's a bad idea, he might know what he's talking about. If Qi-Gong just listened to Yoda and Nick Fury, then Darth Vader would never have taken over the government, The Empire would've never taken over, and Star Wars Episode I, II, and III would be the only-- ...wait, on second thought, good going, Qi-Gong.