Plot hole: An important plot point (in the book and the film) is that Charles Calthrop - thought to be the Jackal, at that stage - played some mysterious part in the 1961 assassination of Rafael Trujillo, the dictator of The Dominican Republic, and rumours of his involvement came to the attention of MI6 and Special Branch, leading to the accidental exposure of the Jackal's false passport. In fact there is no mystery at all about the assassination of Trujillo and there were no shadowy foreigners involved. It was organised by Trujillo's own senior aides, amongst them General Juan Tomás Díaz, Antonio de la Maza, Amado Garcia Guerroro and General Antonio Imbert Barrera. The gunman was later identified as Luis Aniama Tio. All the conspirators except Tio were arrested, tortured, and shot. There was no panicked evacuation of foreigners who were involved with Trujillo's regime, and no reason for them to be concerned - the government did not fall and Trujillo's brother Hector took over as President, ruling in a brutal and totalitarian manner for a further eight years. Any rumours of a mysterious Englishman would have been dismissed out of hand and would not have made it onto even the lowest level filing system anywhere in Whitehall.
Plot hole: There must be a lot of dumb scientists in Sebastian's lab. While defibrillating the invisible gorilla, (s)he becomes completely visible for a moment. However, not once do the scientists consider that applying a mild electrical shock to the system renders the invisible animal visible again - that electricity may be the key to the whole invisibility problem. They don't even comment upon the fact that the gorilla does become visible.
Plot hole: Patrick Redfern needs someone to be in the boat with him to corroborate his and his wife's deception and be his alibi. That is whole point of his wife lying on beach - he gets this when taking Myra for a ride - but it was portrayed as a random ride she got, he did not intend or plan giving her a ride, he did not see her loitering near the boat, or even in view of him untying the boat. Even if that was intention in the story for him to be seen ready to cast off, the movie viewers did not see her viewing him, only her appearing just before he was set to cast off. Without someone with him the whole deception would not work, he would have no alibi, he could have killed Arlena unseen.
Plot hole: Maria describes in lurid detail how Anna was arrested by the Germans and tortured by being severely whipped, leaving her with gruesome scars all over her back. She also says that Anna hasn't spoken a word to anyone since she escaped from captivity. How, then, does Maria (or anyone else) know about the scars? Nobody saw them (they don't exist) and Anna obviously didn't tell anyone about them.
Plot hole: This film is set in 2004. The thought that no search and rescue operations would be put in place after an aircraft disappeared from radar during a routine flight is absurd. The Chinese are paranoid about intrusion on their territory and the downed aircraft would have been located by a simple satellite search within hours of it crashing. Chinese military satellites crisscross the Gobi and they are equipped with optical cameras, microwave and infrared detectors and radar, so spotting a metal aircraft on the ground would be simple even if it was hundreds of kilometres off course. The crew would have been visited by Chinese military helicopters (and probably arrested!) as soon as the storm had died down.
Plot hole: How could Jane not be aware that Tom had only used one camera for the date rape interview, recording his fake tears later? That's the way things are done on television news shows and as an experienced, hard-bitten television producer she could not possibly be unaware of that. The reporter always records his or her reaction shots (called 'noddies') after the interviewee has left. Shooting with two cameras would involve two crews, two lighting rigs, a vision switcher and so on and so on and a straightforward interview simply would not justify such a complex and expensive set up.
Plot hole: The "video history" of the crashed USAF ship makes it very clear that the planet is uninhabited when they "landed". I can understand how a race of apes develops - they had a bunch of them on board. I can understand how a race of humans develops - they are descendants of the original crew. What I don't understand is...where the heck did all the horses come from?
Plot hole: The "death" of the three astronauts and the requirement to then fake the whole scenario of the failed mission was obviously unplanned - it came about because of an unexpected computer glitch which reported that they had burned up on reentry, causing a mad scramble to cover up the fake mission and kill the astronauts. Obviously it was planned to have the astronauts "return" to Earth as heroes after their supposed trip to Mars, maintaining their deception (under threat if necessary) for the rest of their lives. One problem. Every scientist on earth would be champing at the bit to get their hands on a sample of Martian rock. Samples would be worth billions, worth far more than Moon rocks are worth today. How was NASA going to explain they didn't have any? They could not possibly fake the rocks - Martian soil and rocks would have a number of identifiable characteristics that a smart first year college student could identify. Using Martian meteorites collected from the Earth's surface won't work, either - prolonged exposure to the Earth's atmosphere would leave tell tale weathering and chemical changes that would be instantly detectable. NASA have painted themselves into a corner and that is not something they would have failed to realise well in advance.
Plot hole: During the later parts of this movie there is much talk about 'continental displacement' and this appears to be happening in the film. The Earth's crust is falling apart because of the heating of the inner core, and all the cities seems to be falling apart since the ground can no longer hold them. When our cast finds themselves surprised to be already over China when they figured to be over the ocean, it is explained that Asia has actually moved from where it was. If this phenomenon is taking place globally, how come the monks in China don't seem to have been disturbed at all? In fact the bell the monk rings as the ocean approaches hasn't even been shaken. The arks are built in between the mountains, but the mountains are apparently fine. Shouldn't they be falling like the rest of the crust?
Plot hole: Inmediately after Jamie Foxx finds the bomb in the city hall, and he says, "We don't tell the mayor anything", we see Gerard Butler arriving to his property next to the prison, and finally he enters his jail cell. So, in the time between Gerard Butler's arrival to the property and his entrance to the jail cell, Jamie Foxx thought about a plan, picked up the bomb, passed through the traffic and security checkpoints, talked to the warden to get access to the prison, entered solitary, handcuffed the bomb, and still had time to wait for Gerard Butler's arrival.
Plot hole: Considering the incredibly elaborate plans Maddy makes to have her husband murdered after forging a will she knows is invalid so he dies intestate and she - as his widow - gets his entire fortune, you'd think she would have worked out one little fact - Edmund Walker does not die intestate. It is established in the film that the dud will supposedly written by Ned Racine replaces a previous, valid will which bequeaths half his fortune to his niece Heather. When the new will is declared invalid under Florida law the previous will takes precedence and Heather and Maddy split the fortune. In no way will Maddy get the lot.
Plot hole: Peter goes into Carl's mind to save Catherine. When he's in there he sees the tank with the water nymph. On the tank are strange symbols which provide the FBI with the clue needed to find the latest victim. Makes sense so far. But, go back to the scene just after the FBI have captured the comatose killer and are looking in his basement. The FBI are looking at the contraption that the killer uses to suspend himself over the victim. On the contraption is the same symbol seen later on the water nymph's tank. Why didn't the FBI follow up the symbol then?
Plot hole: In the scene where Ashley Judd runs away from her attacker and falls into her aquarium he has moved to the bottom of the stairs - there is no way he would have been able to move that full fish tank. It looked to be about a 30 gallon tank - it would weigh about 400 pounds with the stand and even if he slid it with some superhuman strength, glass tanks are notorious for shattering when you move them full. Plus it would've made enough noise to wake the dead - no way she wouldn't have heard it.
Plot hole: The entire plot hinges on the villain's gang obtaining the tablet that allows admin access to the building's systems. However, it can only be unlocked via facial recognition and it is keyed only to Will Sawyer's face. In fact, when they finally do get it, Xia unlocks it by holding it up to Sawyer's face. So what was the point of trying to steal the backpack containing the tablet? Without Will to unlock it, the tablet is useless.
Plot hole: In any given volume of air, there are any number of tiny, living organisms; dust mites, viruses, bacteria, etc. Why did the teleporter combine Seth's DNA only with the fly that was in the chamber? If he had taken the "floating organisms" into account in his calculations and programming, then why would he not have excluded ALL foreign DNA?
Plot hole: When Vlad enters Mehmed's tent, the entire floor is covered in silver coins and Mehmed remarks on Vlad's weakness to it. There's no way that Mehmed could have known about Vlad being a vampire or about his weakness to silver, as Vlad had killed every Turk after becoming a vampire, so nobody would be alive to tell him. Even the Turk found on the battlefield in the morning lived long enough only to deliver Vlad's message, but died immediately after that.
Plot hole: At the end of the film, we see Edward carving ice sculptures in his mansion. How did he get the ice up there? First of all, it takes place in a warm climate and I didn't see a freezer up there in the castle. He couldn't have gotten ice from town because firstly he had scissors for hands and couldn't have gripped the ice. And, even if by some miracle he could, he wouldn't be able to buy any from town because everyone in town but Kim was convinced that Edward was dead, she told everyone that they killed each other. And Kim didn't bring it to him because she told her granddaughter in the end that she never saw him again after that night. So where did he get that ice?
Plot hole: Had one or more locomotives coupled onto the real runaway's front engine, or even just been pushed by it, anyone aboard the "rescue" engine could have just walked to the unoccupied ones and shut them down - no copters or fireballs required.
Plot hole: Apart from the impressive pyrotechnics, what is the point of destroying the Blue Thunder helicopter? By far the most expensive, time consuming and technically complex part of producing any aircraft is the design and development phase - once the prototype is in the air production is relatively straightforward. The bad guys can make new Blue Thunders any time they like, and Murphy has destroyed the only evidence he has that there was a criminal conspiracy behind the whole programme - the 'videotape' he has of blurry, false coloured characters will convince nobody. Without the helicopter to back him up that tape is of no value to him.