Plot hole: Considering how important it is to the Analyst that Neo stay connected to the Matrix at all times, it is unfathomable that his body in the real world is unguarded. While keeping an eye on him inside the Matrix at all times is difficult, there is no reason whatsoever that he should be left alone inside his pod with no security for even a second. This is an entirely different scenario than the original 3 films where resistance fighters finding Neo was integral to the machine's plans.
Plot hole: What on earth are those sailors doing with Hyde when he is chained up on The Nautilus? He is solidly chained to the floor and walls and they keep stepping up to him to allow him to swat them out of the way, risking injury or even death. They stand around like idiots as if waiting their turn to walk up to Hyde and be belted across the room. Why? Why are they even there? Hyde doesn't need subduing, and if he needed guarding they could do it without getting into range.
Suggested correction: They are there to subdue him because he is strong enough to tear the chains from the walls, which he does seconds after they stop trying.
Plot hole: When Xander is driving onto the bridge, chased by the police cars, we see that there are police cars also blocking the end of the bridge to stop him getting away. How come none of them noticed the ruddy great ramp sitting alone in the middle of the bridge and moved it? It wouldn't take a genius to work out what he might do.
Plot hole: Wouldn't the bomb (when in the back of the truck of the bad guy driving away) vaporize him, considering he wasn't that much far apart than Allison was when she was tied up? He is even quoting as "Are you comfortable? Well it doesn't matter considering you'll be vaporized before you know it," when she was about 4 ft away.
Plot hole: A nuclear armed stealth fighter is accidentally sent back in time to 1940's Nazi Germany. After the Nazis capture it, two days later they drop a nuclear bomb on the United States. There are several basic problems here. Firstly, if the Nazis captured advanced technology, wouldn't they spend more time taking the plane apart and interrogating the captured pilot? How on earth did they manage to train a pilot to fly the stealth in such a short length of time? And how did the stealth fighter manage to reach the U.S. from Germany when in-flight refuelling was unknown then?
Plot hole: When Qiu is leaving Emilien, she ties him to a chair, sitting on a raised platform. This is to make it possible for the big ball to hit Emilien. But, when Daniel arrives, Emilien is able to throw himself into the trunk, which means, that if Daniel didn't show up, Emilien could have just thrown himself to the floor instead. So if he would be off the raised platform, he would never have been hit by the big ball in the first place.
Plot hole: The assassin cuts a hole in the glass to kill the Federation president. But with the size of the hole and the placement of the scope on the phaser rifle, the assassin would not have been able to see out of the hole.
Plot hole: When Marty lies on the conveyer belt on the way to the stone crusher he tries to wiggle off the belt. The little he seems to be able to move is not justified by the way his hands and feet are tied up. (01:08:30)
Plot hole: Bond goes after Lupe after she leaves the casino table, and they have quite a lengthy, hush-hush conversation. It's a casino, and there are cameras everywhere. Certainly, this would have been brought to Sanchez's attention since he was already leery of Bond and possibly Lupe.
Plot hole: In the scene where Katrina is watching through Valek's eyes as he kills father Molina, Crow orders father Giteau to "find out where an old padre is missing". But Katrina never described father Molina, all she said was "He killed the priest". Crow could not have known the age of the man who was killed.
Plot hole: Slater decides to render the nuke inert by punching in the wrong code three times. However, when he does this, the nuke becomes armed, and Travolta reveals that he is one step ahead by having used a special kind of circuit board to produce this result. Two questions: One, once Slater has armed one nuke, why not arm them all? You've got nothing to lose, and you can keep Travolta from getting them for whatever evil purpose he has in mind. Slater plans to send them all to the bottom of the copper mine anyway, so just arm them all. Two, Travolta later arms a nuke himself, and then smashes the keypad with his gun. Well, if you can do that, why doesn't Slater just smash all the keypads as soon as he gets the nukes? Travolta would be defeated; movie over.
Plot hole: Calden would almost certainly not be allowed into the autopsy room without some protection: a facemask, goggles, gloves. Not only to protect from errant bodily fluids (as we saw) but also to protect from any infectious diseases those fluids (or any escaping gasses) might carry. Also, he runs the risk of contaminating the evidence.
Plot hole: In the lobby of police headquarters, Danny Roman's lawyer tells him to make a deal with the prosecution. Danny turns to his wife Karen and tells her to wait in the car and he will be right back. Then he proceeds to go upstairs and overtake Niebaum's office. Much later when Chris Sabian is negotiating, Karen arrives on the scene wondering what's going on. How long was she waiting in the car? (00:28:35)
Suggested correction: This isn't a mistake. Karen (and anyone else still on the property) would have been sent away by the police once they became aware of the hostage incident. She went home to wait for Danny because she doesn't know he is the perpetrator. When she is called back to the scene by Sabian she wonders what is going on because she doesn't know that Danny has taken hostages in the building.
So she drove there with him and then just leaves him there? Lol. Can't see her just leaving without him since they drove there together. Even if people went around telling everyone to leave the area, I just can't see her not hanging around and waiting for him.
Plot hole: Doug begins to land on the air strip after his father has been moved. But note, the Hades bomb had not yet been dropped. If his dad had not been shot at that moment, one can assume that he would have finished his landing and been a complete sitting duck when he has to get out of the plane. What was he saving the Hades for at that point? It is only later when he actually drops the Hades that he barely has enough time to rescue his wounded dad.
Plot hole: As the characters arrive at 'the Jar', Brill informs Dean that it is entirely cut off from the outside world (no communication lines or radio waves). Yet somehow he is able to access a Government database from this very location.
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: The premise of the entire movie's main character, played by Jeff Bridges, is flawed, as it would be impossible for anyone to pass a major metropolitan police department's pre-employment screening background investigation for the position of police officer if that applicant uses a fake name and identity. Part of the investigation includes sending off the applicant's finger prints to the National Criminal Information Center, a polygraph test, a records check with vital statistics to verify place of birth, Dept. of Labor to verify past employment, Social Security Dept. and also interviewing (sometimes in person) your friends you've listed and your current and former neighbors of where you now live and use to live.
Plot hole: Everybody jumps into the water and emerges on the submarine except for Natalie. They're wondering where she is when they notice a flare. They realise it's her, and they send a search party. She's hiding on a bus maybe one to two kilometres away from the water. Her going there makes no plausible sense. Makes no sense how she held her breath underwater longer than anybody that they didn't see her and why she would go in the opposite direction of the sub. It was done to prolong the scene. (01:09:00 - 01:18:00)
Plot hole: How would Arnold know about the cop hitting the bus when he was running away from him during the parade? He was far past him at that point.