
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: 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 Tomahawk Cruise Missiles the Arleigh-Burke Class destroyers carry have a range of approximately 1500km. As soon as Alex got the message from Sam, they could have blown that Saddle Ridge communications facility to kingdom come with just a few cruise missiles. They didn't need to get in range because the entire dome surrounding the Hawaiian Islands was smaller in diameter than the range of the Tomahawk Cruise Missiles. Cruise missiles have internal guidance, so they wouldn't rely on the radar, which was jammed.

Plot hole: There is no reason at all why, being targeted by a few arrows by unseen enemies - a fire suppressed already by the salvo of their own archers - the Rourans would turn around their heavy siege equipment, away from the bulk of the enemy forces, and fire it, hurling a single heavy stone to the middle of nowhere when they have the whole rest of the army who could storm the rock the supposed enemy commandos hide behind, or the archers who could keep shooting - again, they proved to be completely successful. It also makes no sense that the all-powerful witch who made the warriors flee managed to do any of this, 'sneaking' by horse in the middle of the steppe.
Suggested correction: Mulan used the helmets of the fallen warriors to make it appear that a large force has flanked Rourans. Rourans didn't expect this new "force" and knew nothing about it. They didn't know its size. And while their original target seemed harmless, this new "force" was killing Rourans. Fear and death were the reasons. What you see in this scene is an enactment of one of Sun Tzu's famous quotes: "All warfare is based on deception. [...] Attack him where he is unprepared, appear where you are not expected."
What we see in the scene is laughable, and not because of the idea, which surely is based on the profound strategic motto you mentioned and we find in many folkloric tales in other cultures as well; what we actually see in the movie, is that she grabbed a couple helmets lining them up on a rock, and she shot a few arrows. Then she stops shooting, and we see helmets knocked down in their full view. The movie truly surpassed itself in showing it in the most phony way; had they shown her shooting from behind the rock responding to their fire, or the helmets not falling, or them just shooting at mist, terrified, it would have maybe worked. It's an enormous overreaction. That and, under no circumstance trebuchets are used that way anyway. And she did all this setup unseen, again.
In response to death, nothing is an enormous overreaction. Something or someone was killing them. They wanted to kill it, and they didn't have time for Facebook's famous brand of pseudo-myth-busting. What if they knew it was one girl shooting at them? They'd still have done the same. Being killed is a very personal matter.

Plot hole: Sea-Plane tells the group that he has tried twice to cross the canyon and complete the transportation level. It would have made no sense for him to be completing that level moving toward the jaguar if he didn't have the jewel needed to finish the game. Either he had been given a jewel and it was reset back and given to the new players or there could be more than one jewel in the game but he doesn't mention having his own jewel.

Plot hole: Spoiler! We find out that "Rogue" is actually Tom Lone, who killed the real Rogue and destroyed his face to prevent identification, then had plastic surgery and went underground to get revenge. But how is the body never identified? Lone was a cop, they'd have blood type, DNA etc. on file, which would have proved the body wasn't his.

Plot hole: Mola Ram has his men knock over a vat of water in a last ditch effort to kill our heroes. First of all the vat can't be that big if it can be knocked down with a few sledgehammers. Secondly, for the amount of water that chases Indy and co. down the vat would have to be big enough to fill the room it's in, which obviously it's not. Third, Indy and co. travel through several large caverns during the mine cart chase, caverns that could easily swallow up any of the water flowing through the tunnels so there shouldn't be any water left to catch up to Indy by the time they stop.

Plot hole: It's assumed that Dr. No had Professor Dent slip the spider into Bond's hotel room that night but if it were that easy to do that then why not just hide an assassin in the room to begin with. Someone had to be in the room to tamper with Bond's briefcase, the closet, and possibly the bottle of liquor so just hide an assassin instead of waiting for the spider to kill Bond. (00:40:00)

Plot hole: Why on earth do they drive the Minis up the ramps into the bus while it is moving? They are on a long, straight, relatively quiet stretch of road, but there are cars and buildings about. That ramp is going to make a noise like the sky coming down (we see sparks as it scrapes on the road) and they put on a display anyone would be, frankly, amazed to see. Don't they think one single person would call the police? Don't they think that reports of three brightly coloured Minis will be connected with the recent robbery? They cannot possibly think they have to load the Minis on the run in order to elude the police; they have lost the police cars and are no longer being pursued. Why not just park the bus on the hard shoulder and drive the Minis sedately up that ramp? An unusual sight, maybe, but nowhere near as clumsy, obvious and attention-getting as the way they do it. They are asking to be pulled over and arrested.

Plot hole: I have never seen a Daytona 500 race where the winner is immediately left completely alone and is able to walk over to his crew chief who is still at the pit wall and hold a quiet conversation.

Plot hole: Superman traps the supervillain (whose power depends on sunlight) inside of an elevator to incapacitate him. Superman then ripped the elevator out of the building. He then plants it on the far side of the moon. Later on, sunlight starts to shine into the elevator through a slit at where the doors meet. The villain of course recharges and comes after Superman again. Now, if light could get through that crack there, then why couldn't it get through when the elevator was ripped out of the building in BROAD DAYLIGHT?

Plot hole: When Indy and Sallah visit the gentleman who translates the staff headpiece for them we hear the staff should be "six cadams high." Indy replies, "About 72 inches." Then, turning the headpiece over, "Wait - take back one cadam to honor the Hebrew God whose ark this is." It's definitely referring to the staff length - Indy says afterwards "Their staff is too long." So, about five feet now, right? But, when Indy goes to the map room the staff is much taller than him. If the staff is about five feet high, Indy would be around three feet tall. (00:48:25 - 00:53:05)

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?

Plot hole: When Diana turns up at her director friend's house she finds it crawling with cops as his girlfriend Christie has been murdered and the house is now a crime scene. She explains she lent Christie a coat and is there to pick it up - and a cop helpfully finds it on the floor and hands it to her. Are we to believe that a homicide policeman will hand over an artifact from a murder scene to an unidentified woman without making any attempt to confirm her identity, or even if the coat is even hers!? They don't even ask.

Plot hole: Bond would not have had (nor taken himself) time to lay a complete and careful clown make-up while changing clothes in the circus trailer.

Plot hole: Even if boys of that age had the technical know-how to quickly repair Jeeps over 20 years old (seriously?), any gasoline in the tank would have long become unusable, the tires and lines would have rotted away, and the electrics would all be dead. Now if it was in the desert or a dry garage, it may have survived, but it's on a tropical island, in a shed that has all sorts of holes in the roof, leaving it exposed to every kind of weather the island could throw at it. In addition, the kids start the jeep with the small battery of an ATV, which cannot produce enough power to crank a Jeep engine.
Suggested correction: It is not uncommon for youngsters to want to help family members when fixing cars, it also wouldn't take much to know how to change a battery and put some fuel in. The gasoline came from the crashed ATV outside so it is therefore fresh. In regards to the age of the vehicle, it is not known when it was last used. It could have been used by builders whilst Jurassic World was under construction. Judging by the difference in condition between the garage and the main rotunda, it looks like the garage has been somewhat maintained which would back this theory up. It is also worth noting that the Jeep was left to rot after filming and that is genuinely the condition they found it in, apart from putting new tires on it they didn't have to do any mechanical work to get it running so it is indeed possible to get a vehicle running that has sat for years. In regards to the battery, there have been huge advances in technology. I have a classic Capri which used to use a huge lorry / forklift battery. It will now start off a battery from a 2008 Ford Focus.
No it isn't possible to get a machine that's been sat for years without first repairing it, especially since machines that have been sat for years become non functional due to the damage by the effects of aging.
I'm a mechanic and can confirm that a car will start after many years without "repairing it." Yes it won't start as easily as the Jeep did in the film, but it will definitely start without needing to replace anything other than fuel and the battery. There's also plenty of videos on YouTube of people starting cars that have sat for years and years.
Anyone who thinks the jeep wouldn't start should head over to youtube and watch some barn find videos. That jeep was immaculate compared to some of the things you see start up for the first time in decades on youtube.
There's a road leading right to the garage, one Claire knows about because she says it leads to the new park, it IS overgrown but no tropical trees have sprung up in 2 decades, it all kinda suggests those jeeps might have been used far more recently. The truth is, we don't know. It could have been 20 years, 2 years, or some park employee had a pet project and it was 2 months since they last ran. Someone had been in there to replace the night vision goggles' batteries.

Plot hole: When we see Sentinel Prime being extracted from the Ark by Optimus, we can see that Sentinel Prime already looks the same way as he does throughout the rest of the movie. The Ark crash landed in the 1960's, the Rosenbauer Panther Fire Truck didn't exist in the form we see Sentinel Prime transform into. All of the other Autobots came to Earth in their proto forms and adopted a disguise when they arrived [we see them scanning alternate modes - one Decepticon is shown doing likewise in this movie.]. Sentinel Prime already has his disguise when on the ark, which isn't possible.