Plot hole: Swapping his dental X-ray records with his deceased partner won't convince anyone that Varrick is dead - then (as now) the patient's name appears on the X-ray.
Plot hole: In the air vent, we see a rat. Wouldn't rats in the vents set off the alarms on a regular basis, because the lasers were on the upper side of the vent?
Plot hole: SPOILER: When Amy comes back, doctors would have checked her non-existent head wound from the "abduction", from where she supposedly lost that much blood. That would and should have revealed all of Amy's lies.
Plot hole: Where did Cross get the blood on his hands? The gloves were clean of blood after he looked at the teeth and removed the gloves, so where did it come from?
Plot hole: When Ben Affleck is meeting with the man who changes Samuel Jackson's credit record, the man remarks that Samuel Jackson should not have told Ben Affleck that he was in insurance. Samuel Jackson never told Ben Affleck that he was in insurance.
Plot hole: When Terry gets back to her computer, after escaping from the spies and cops, the time is after 3pm New York time. If Jack actually is in Russia or Eastern Europe, wouldn't he have already gone to, and been killed at, that 5pm meeting?
Plot hole: Andy is suspected of having killed Eddie Caputo, because he was at the scene when Eddie's house blew up and Eddie was killed. But there are glaring things that go unquestioned: None of the cops seem to think it's strange that a six-year-old kid would travel by himself so far to some random house in order to blow it up. The South Side neighborhood where Eddie lives is halfway across the city from Andy's apartment. How did Andy know where Eddie lived? How do the cops think he even knew Eddie at all? None of them address this most puzzling problem.
Suggested correction: The police believe Andy to be insane (hence why he is sent to a mental institution instead of juvenile hall), and thus do not believe his choice of victims to be in any way rational.
Also, as unlikely as it is that a six-year-old child could (or would) travel halfway across the city to murder a random person, the possibility that a child's doll came to life and carried out the act was considered far too outlandish at that point in the plot.
Suggested correction: We don't see the entire investigation. We just see the cops holding Andy then taking him to a psychiatric clinic. Chances are they were asking those questions and we just didn't see it because it's not important to the plot. Regardless, the cops have every reason to believe Andy either knows about or was partly responsible for the murders considering he keeps showing up at murder scenes. There's only so many conclusions you can draw, even if they don't make sense.
Plot hole: When the Drakes (Bobby's family) arrive home they are acting quite naturally, until they find Wolverine there and get a start. Later on we see that they had parked their van in the driveway right behind Cyclops' car, which Logan and company had borrowed and parked there. Wouldn't they, seeing a strange car in their driveway, be suspicious or at least enter their house asking "Bobby, are you home?" (00:52:45 - 00:59:15)
Plot hole: When The Penguin is controlling the Batmobile, Batman punches through the floor to take off the transmitter. We still see a video feed of The Penguin. Why? Batman pulled off the transmitter, so there is no reason for there to still be a video feed.
Suggested correction: We see the Red Triangle gang spends a while fiddling with the Batmobile's workings before installing the transmitter. It's likely they made multiple 'modifications', thus the transmitter was for controlling the car's engine and steering, and the video feed was made possible by another, separate means.
Suggested correction: I concur with the other correction. There are multiple shots showing the gang working on the car and doing other things to it beyond just putting on the transmitter. (You see them playing with wires, moving parts around, etc.) Hacking into the computer/video-feed so Oswald could taunt Batman is likely among the other things they are doing. There's nothing into the movie that suggests taking off the transmitter should (or even could) interrupt the video-feed. The fact that Batman has to punch the screen to get rid of the Penguin's image is another point to the fact that the transmitter itself had nothing to do with the video feed.
Plot hole: The idea that Ben Gates had to run away despite the President's being okay with the kidnapping does not make sense. The President could simply pardon him if necessary. However, when he ran away, he would likely be committing other crimes (fleeing and eluding police, reckless driving, etc.) that would not be federal crimes and so would not be pardonable.
Suggested correction: That's basically what he did at the end. Even though the President was OK with Ben "kidnapping" him, if Ben didn't find the lost city of gold he would have been arrested and charged for kidnapping the President (amongst other charges). However, because Ben was able to find the city the President gave him and his crew a full pardon and explained that it was a misunderstanding.
Plot hole: The motivation of the cult in this film - a dark entity trying to birth their demonic god - is completely different from the cult of the original film, which was portrayed as fanatical Christian witch-burners. No satisfactory explanation is given in the film to explain this and in fact the film explicitly implies they are the same cult on several occasions. The explanation that the cult of the original film is some sort of offshoot or different sect of the cult from this film cannot explain this as it is pure fan speculation and conjecture (thus non-canonical) and in fact raises several more plot-holes.
Plot hole: It makes absolutely no sense that there would be over a dozen cops and soldiers in the lobby of the courthouse and leave only two cops to guard Lecter regardless that he was locked in the makeshift cell. Yes the plot needs a reason for him to easily escape but this still goes against every conceivable protocol for such a dangerous prisoner especially when there were dozens of armed personnel just in the scene alone when he was being transferred from the plane.
Plot hole: There is no logical reason to switch off the Bombe at midnight when the codes change. Firstly, Turing's proving the concept of automated code breaking, so even if it only finds the right settings days or weeks later, the experiment is worth doing, then you can work out how to speed it up to be operationally useful. Secondly, even in steady state operation, cracking "yesterday's" settings (and thus intercepted signals) is still going to be pretty useful in most cases. Threatening to smash the Bombe up at midnight is good stuff to add some movie tension but, in reality, it's nonsense.
Suggested correction: It's not a plot hole, it's how they operated it in reality.
I have a copy of British Intelligence in the Second World War, by F H Hensley (the official historian and ex-GCCS). I quote page 309 as an example - 'the knowledge of the Tracking Rooms was far from perfect on account of delays in breaking the settings...During the first half of 1943, however, while the traffic was read with delays that were sometimes less than 24 hours, days when the settings proven to be unusual stubborn were not uncommon...Between 10 March Andy the end of June the setting standards for an a further 22 days were either not broken at all or broken only after a long delay.'...'A delay of as much a said three days in learning that U-boats had been ordered to move to new position so could thus mean than intelligence was received too late to be of use in diverting convoys'. So pretty clear that they carried on attempting to crack the settings well after the end of a day so they can process intercepts which might still be relevant.
Plot hole: Tommy leads the mob after the 2nd escaped patient, thinking it's Michael, but Tommy should have known it wasn't Michael. He saw the patient on the TV at the bar at the beginning of the film.
Plot hole: When Evan is in jail with the religious prisoner trying to get him to help him get his journals back he goes to the scene where he is drawing that homicidal picture in kindergarten, but he gets up and puts the spikes that holds documents through his hands, creating a stigmata-style scar. The religious guy in the cell with him is so amazed because of this he thinks Evan is a prophet and he decides to help him. If Evan had gone back in time and got those scars on his hands, he would have changed the original timeline and would have arrived in jail with those scars the whole time. Some people try to correct this using the "If I can create scars, then can I fix them?" statement Evan made to defend the mistake and suggest he can create instant scars but he was using the word "scars" to refer to the negative events; not literal scars on his body. The scar he got when he burned himself in the past didn’t magically appear on him the moment he returned from the past; it became part of a new, slightly altered timeline (just like the scars on his hands should have been) and it let him know he can change history.
Suggested correction: This isn't necessarily a correction so much as a possible explanation. It's possible that the religious inmate (I think his name was Carlos) just simply didn't see the scars on Evan's hands when he first came to the prison in the timeline where he got the scars or Evan knew to hide them in the scar timeline (due to the fact that it was the sole purpose of him going back) and due to his fanaticism he didn't question him a second time.
Nope, after jamming those things in his hands Evan simply came into the prison with the scars already on his hands and would have never thought of showing the religious guy his powers using that particular moment in the past to convince him, or doing what he did a second time as he already had done it. It doesn't matter if the religious guy didn't see them before, they won't be the object of Evan convincing him. He would have had to try it some other way, each and ever time. That how this time travel works and its definitely a plot hole that it worked as it did, whilst it shouldn't have. Of course, it's a time travel movie and they never make sense.
Plot hole: When Tim Robbins is floating away in space his wife could have easily saved him. She could go out a little further, use the grappler to catch her husband, then use the fuel she has remaining to halt their acceleration towards the planet and return them partway to the necessary orbital altitude/velocity to rendezvous with the resupply module. Then, Gary Sinise could come out partway to them using his thrusters, Connie could shoot the grappler out to him, and he could reel both Connie and Tim Robbins back in to the resupply module.
Plot hole: Toward the end of the movie, it is revealed that Silvia spent the night in the secure room where the Matabo President was taken after the assassination attempt so that she could be alone with him and threaten to kill him. With the U.N. and Secret Service on alert for an assassination attempt, wouldn't they have swept the secure room right before the Matabo President arrived that day? In addition, Silvia would have had to use her access card to get in that area of the building, so there would be a record of her being in the building but not at her station. Wouldn't that raise some suspicion long before Tobin figures it out?
Plot hole: When Hooper and Chief Brody are trying to get the Mayor to re-close the beach after finding Ben Gardner's boat, they fail to mention they also found Ben Gardner's severed head. The Mayor would be forced to re-close the beach if yet another confirmed shark fatality had been mentioned, but Hooper and Brody never bring that important detail up. [This is still a mistake, but the explanation for this is that the scene where they find Ben Gardner's head was not in the original script. Originally, they just found his boat. Spielberg felt the scene needed a little more shock value so they shot the part with the head in a swimming pool long after the main filming had been completed.] (00:50:20)
Suggested correction: First off, it wasn't a severed head as you can still see the body attached to it, and second, what difference would that make? Two people and a dog already died, with the death of the Kitner boy being witnessed by several people, and the beaches still stayed open because the mayor was too stupid to close them. Not only that, but during the scene you mentioned, I believe it was Hooper who said that THREE incidents had occurred BEFORE the third killing takes place on-screen.
And not only that, but the mayor witnessed Hooper saying that the shark they caught was not the same one, or at least it was possible that it wasn't. Either way, shark attacks were happening, but the mayor did nothing about it.
Plot hole: When the President of the United States attends a public gathering (such as the SuperBowl) the level of security is extremely high. So why wasn't Mason's delivery on the day of the game checked for explosive devices?
Suggested correction: This isn't a plot hole. It's just your unfounded assumption. There's no evidence to support the supposition that the T-X has such audio detection capability.
Even if she could detect it, how could she discriminate between the sound of Catherine breathing and that of the dozens of caged animals in the room? That's stretching even fictional technology a little far.