Minor Plot hole: Timing is an art ! The film demonstrates again and again that the deadly toxin affects the host’s body almost instantly as soon as it is inhaled. And yet the league of shadows who were the ones who weaponized the toxin saw fit to start the focused-microwave machine in Gotham without their gas masks, inhaled a few waves of the deadly air, and THEN decided to put their masks on. Good move soldiers !
Major Plot hole: Near the end of the film, Batman grapple hooks onto the moving train so that he can fight Ra’s. However, Batman had just sent Gordon to destroy one of the monorail supports so that the train couldn’t reach Wayne Tower. So why did Batman even need to get on the train? And furthermore, why didn’t Ra’s just start at Wayne Towers? He said they had “infiltrated every level of Gotham’s infrastructure,” so surely they would’ve had access to Wayne Tower.
Super Plot hole: The league of shadows had the perfect plan to destroy Gotham. By sneaking-in a toxin in the water supplies for weeks before revealing their machine and its purpose, their tactical supremacy was everything but challenged. That is…. unless a single person out of the millions of Gothamers used boiled water in the past few months. But what are the odds of any of them taking daily showers and cooking food ? Exactly. None. And that is off course hiding the other tiny problem of human bodies being composed at 60% of water.
Plot contrivance: The league of shadows had the perfect secret base. It was made mostly out of wood, and it stockpiled a gargantuan amount of explosive powder right in the middle of its infrastructure in an open room with no security measures to either contain or block potential fires and explosions. What could possibly go wrong with that ? Exactly. Nothing.
Plot Contrivance: In Batman’s Universe, fire burns deadly fast. It takes roughly 1 minute for a little fuel-induced fire on carpets and furniture to reach the top of Wayne’s Manor and make a large 200-hundred pound wooden beam fall on Bruce Wayne. Holy shit Liam Neeson controls fire !
Plot Contrivance: Fancy Gotham Theaters do not have exits in front of busy and somehow secured streets. Instead, the rich families who want to leave the Theater need to leave through a dark back alley with no staff checking the doors – which is very useful for a criminal loner in need for some quick robbery with no consequences.