Plot hole: When Bond and Scaramanga are duelling, Bond has no tie or jacket on. After Bond drops his gun and gives his hiding place away, he somehow has the time to not only crawl back onto the staging but to move the wax replica of himself and also to put on the dummy's jacket and necktie.
Plot hole: During Howard's flashback the viewer sees from his point of view the two SS agents who had been following Enrique fire multiple shots at the now revealed Spanish police officer as he was talking to another police officer (Javier) who had just approached him. The scene ends leading the viewer to believe Enrique was killed by the SS agents. However, in the final scene when it's revealed that he was in fact killed by Javier the SS agents significant fire (9 shots I counted) and presence is completely forgotten. (00:40:00 - 01:12:00)
Plot hole: The government would have no chance of hiding the existence of the comet for a year. Most comets are discovered when they are very faint, literally thousands of times fainter than Wolf-Beiderman when Leo found it. Long before the events in the film take place, probably even before the government itself would be notified, the comet would have been discovered, an orbit calculated, and people panicked. The whole premise of the first half of the movie is thus based on flawed logic.
Suggested correction: Only 3-4% of the visible universe has been discovered. Meaning this comet could have been discovered much later.
Plot hole: If they assembled the wet bike on the submarine, they wouldn't be able to get it off as it would be too big to fit through the hatch.
Plot hole: When the bomber is surrounded at the end he gets shot in the leg but manages to get away from all of the police that were surrounding him. They were literally an arm's length from him.
Plot hole: At the end, when Chris finds the informant's phone, he sees that there are 2 voicemail messages. Instead of listening to them, he calls the last number, which reveals Abel is responsible for the break-in when he answers and in turn reveals to Abel that Chris knows about the break-in. It would make more sense to just listen to the voicemails, as Chris became immediately suspicious when he saw them. Considering Chris called the last number, he must have known that the last number was also the person who left the voicemails. Very deliberately done to bring realizations between Chris and Abel for a climax.
Plot hole: After the scene at the Houses of Parliament where Irene Adler escapes through the sewer from the clutches of Lord Blackwood, she suddenly appears at Tower Bridge, about 3 miles away. Even assuming she ran there and the journey was skipped, going there makes zero sense. It slows her down, leaves her exposed and limits her exit points - she's got all of London to escape into! (01:48:00)
Plot hole: Bobby confronts Wilee on the college campus to give him the envelope. Whilst the confrontation progresses, Wilee gets away from Bobby after distracting him by holding his sandwich by riding his bike off the college campus, onto the main road and never stops. During this ride, he drives past the gaps in several cars and taxis. Within a minute and a half, Bobby then manages to catch up with Wilee. There are two things wrong with the time it took Bobby to reach Wilee. First, there were loads of cars that we would had to have drove past in order to get to him. The problem with this is that Wilee managed to get past the cars using his bike to go through the gaps. Bobby had his car which meant he couldn't have possibly gotten through the gap making him reach Wilee in that amount of time. And second thing wrong with this is, even though Bobby knew where Wilee was taking the envelope too, he still didn't have any way to know the precise direction Wilee was going in to deliver the envelope. (00:11:50 - 00:13:30)
Plot hole: Ruthven is apparently bitter that he has been denied his chance of becoming an immortal vampire after Clara steals the map from him, which is why he attacks Eleanor. But why doesn't he just go to the island anyway? You don't need to be invited - Clara, Eleanor and Frank aren't. Having been there once, it seems highly unlikely he can't find it again - he's a naval captain, so navigation and observation are major professional skills for him. And it isn't hidden or magically protected - the local boatmen know where it is and are prepared to take people there, although they won't set foot on it themselves. He could quite easily have gone there without the map, entered the shrine and been turned into a vampire if that's what he wanted.
Plot hole: In Tokyo Drift Twinkie tells Sean that Dom has been racing and beating drivers around Asia, but in this film Dom only goes to Tokyo for day or two as he tells Mia to tell Brian that he will see him in Los Angeles in two days.
Plot hole: Sang-hwa forces a zombie inside a toilet stall. The zombie begins to bang on the door violently and Sang-hwa has to hold onto the door in order to stop the zombie from getting out. However, it is revealed later on that the zombies do not attempt to attack the humans or react violently or aggressively if they cannot see them. If this is the case, then this scene of the zombie banging on the door even when it cannot see any of the uninfected humans contradicts the rules that are established later on. (00:25:48)
Plot hole: Benji puts his car into automatic mode, which operates partly through satnav. Surely, this would be monitored by The Entity, who has predicted every other action up to that point. The same car is used at the end of the film, but if The Entity hasn't noticed it by then, it's not as powerful as they think it is.
Plot hole: There's absolutely no reason why Kruger had to page Lee from the plane after he'd been drugged. The bad guys had no idea where Lee was until he did that and they traced the phone call. Not only did Kruger give away Lee's location, but he also gave away the only thing keeping the bad guys from killing him.
Plot hole: Near the end of the film Drax tells Bond he had his own shuttle hijacked because he needed it after another shuttle malfunctioned. OK then why didn't Drax just contact whoever he needed to before the Moonraker left on the 747 and have the working shuttle returned to his base before it left. He obviously had the time to get two of his people hidden in the shuttle so a few phone calls would have fixed his problem and the British government would have never had to involve Bond at all.
Plot hole: How does Agent Lahiri know that you needed to raise the pylons before it was possible to make the cross bow shot the boys needed to unlock the house in Amsterdam? Additionally, those pylons would not be accessible through water as they are planted in mud under the foundation of the building, not water.
Plot hole: When Arnie is taking off his woman's head he presses a switch by the ear and the ear comes out. The device reaches right inside the fake head and there would be no room for Arnie's real head. (00:46:00)
Plot hole: Farley Granger meets a math professor on a train bound from New York to Washington, and is able to prove as much to the police. The professor got on in New York and got off in Wilmington, DE, while Granger boarded the train in the fictitious town of Metcalf, NJ, and rode on to Washington. Thus, they met between Metcalf and Wilmington. But the police say Granger could have boarded the train in Baltimore, by which time the professor would have gotten off and they never would have met.
Plot hole: After Sid and her friend get out of the car, they run away from it. Yet somehow while they are talking, the killer climbs out of the car and ends up behind them without them seeing a thing.
Plot hole: Silva spent years planning his revenge against M, yet the ability to carry out his plan depended on conditions that were entirely out of his control, such as being captured by MI-6 despite having no way of knowing that Bond was coming for him, and only escaping custody because Q triggers the Trojan - there's no way Silva could predict when that would happen, could have been hours, days, weeks, or never. He then ambushes M at the courthouse despite having no way of knowing that she would be there that day.
Suggested correction: His plan was always to blow a hole in the tube to have a train crash at that location. This would have caused mayhem and take up a lot of resources (police/ambulance/fire). Bond chasing him had no impact on this part of the plan. Then when his team picked him up, his team would have known where M would have been on that day and would have driven him there. With resources on high at the train crash site, it would have made it easier to reach M.
This aspect is a bit of a plot hole for me too - one of the factors outside Silva's control is when he can escape MI6 custody, which depends on when Q triggers the 'Granborough' Trojan, which Q only spots with a bit of help from Bond. That triggering could have been hours, days, weeks or never - pretty fraught with risk to rely on individual(s) making that happen at a plot-convenient moment... otherwise Silva has a bunch of associates hanging around London for a few days permanently on a few minutes alert for a random event.