Plot hole: When Morgan and her Slave/New Boyfriend are escaping from the burning ship, which is going to explode any second, they emerge onto the deck, run up a flight of stairs, cross the deck to the stern rail, look about themselves, then dive overboard. They know the ship is about to explode and are desperate to get overboard. The railings are about a metre away from the hatch they emerge from in the first place - why not just jump overboard there?
Plot hole: When Vers arrives at the bar, Nick Fury is already there. She went straight to the bar after stealing the bike, while Fury needed still to learn about the theft, link it to the case, with investigations taking place to maybe (only possibility that would not depend on the vehicle being reported) figure out that Pancho's was the destination from examining the search history of the browser. Fury went there by car. His boss also explicitly says to work on the case alone. Amazing he could be there with such timing.
Suggested correction: Vers probably got lost and had to wander around to find the place.
I can't realistically say it's impossible (it is not shown, after all), but nothing in the movie implies it, and it's the exact opposite. She is shown, driving, fast, on the Sierra Highway, which is where the bar is. Not stopping to ask for directions or at crossroads (something it takes 1 second of movie to show). In perfect Star Trek tradition she can speak the language, she reads the maps just fine, in fact she already looked the place up on the map, that was next to her and she already knew how to use without help, before taking off on her fast bike not hindered by traffic. And again, the head start she has is huge since Fury can begin investigating only once he hears about the stolen bike. Fury is at his HQ and a long time seems to have passed, since he is patched up and a whole autopsy has been done. Vers started searching right away.
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: 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: 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: 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 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: 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 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: 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: 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: 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: As the island is sinking you can see parts break off, like the island is falling apart, but if it does this every 70 years then there wouldn't be an island. It should have completely fallen apart hundreds of years ago.
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: 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: 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: The newspaper headline showing young Alex being rescued from a crate is dated April 8, 1972. In the next scene, we see young Alex dancing in the Central Park Zoo, and watching him are Marty, Melman and Gloria as baby animals. This makes no sense at all. In the first film, Marty celebrates his tenth birthday. Key word: tenth. It is also known that the scenes of the main characters as adults take place in the present i.e. Alex confessing to breaking Marty's iPod. Seeing how the animals age quicker than humans, Marty, let alone his three friends, would have to have been born in the mid-1990s and the flashback scenes could not have taken place in 1972.
Plot hole: Nile checks the gun Andy gave her and realises it's empty, which in turn leads her to realise that Booker was setting them up, because he gave that gun to Andy in the first place. No way that Nile, a marine, and Andy, a timeless warrior, somehow both missed the noticeable difference in weight between a fully loaded pistol and an empty one.
Suggested correction: That is only true if you handle the same gun all the time. Throughout the movie they shoot dozens of different guns, all with their own loaded/unloaded weights. Different guns are also made of different materials, and mixture of materials, which would change the weight. Different guns are also balanced differently, depending on the materials and manufacturer. The weight difference in a lot of the guns they were carrying between loaded and unloaded were between 3.5oz-7oz (which is not that much). With all the different guns they use and carry throughout the film, it is not a mistake that they wouldn't catch it. Also, Nile is used to carrying an M16 or M4, not the handgun used in the film so she would have no way to know the loaded vs unloaded weight. They would also not expect someone in their team to betray them, so there's no need to check the weapons (although you should check any gun that is handed to you).
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.