Plot hole: When Ann and Runaway are fleeing from the dinosaurs in the car, suddenly a fence flaps into the screen and blocks the ways of the running dinosaur. This makes no sense and is never explained, since none of Ann's friends or anybody else is anywhere around there to manage this, nor is the fence ever mentioned, nor is there any other (reasonable) reason that the fence would block the way exactly in this moment.
Plot hole: The same zombie who can smell through a vault that Gerry is not worth a bite, just minutes before couldn't smell the presence of three alive humans two meters apart.
Plot hole: After being hit with the spores, Cobra Commander cannot walk or even move very well with any speed at all. The Cobra minions have to drag him to their prison with the Joes and just leave him there on the ground after the Joes make a break for it. The Joes go quite a distance to engage Cobra. Road Block is delayed only a couple seconds behind the other Joes when he is grabbed, but knocks out the minion who grabbed him. Suddenly, Cobra Commander is at his feet telling him to wait because it's a trap. Later, Road Block has to carry Cobra Commander because he still can't move much. There's no way Cobra Commander could have caught up with Road Block to warn him of the trap. (00:52:50)
Plot hole: Once Time Trapper has been stopped by Dawnstar and the time vortex in the sky stops sucking things up, everything in the air just hovers unmoving completely. Except for the people. Somehow Batman and Robin and Superman are able to move around just fine in the same time and gravity frozen place, Robin even jumps from hovering rock to rock without them moving. In fact, as soon as the sucking stops, the tree that Karate Kid is hanging onto stops moving and does not fall, but gravity somehow instantly affects Karate Kid and he almost falls off the tree and has to catch on again. It makes no sense at all for the objects to be affected and stand still and the heroes to not be.
Plot hole: Nick Fury wants to detain Tony as he is the only witness. Tony takes off and Nick Fury even says to apprehend him so their only witness isn't killed. Yet when the S.H.I.E.L.D. robots confront Tony at Pepper's vacation spot, they say they are authorized to use deadly force against Tony. And Nick Fury even orders them to fire when Tony resists. If they need Tony to keep their only witness alive, why try to kill him when he doesn't cooperate? (00:31:05)
Plot hole: There is no way Anna could know that Hester was going to be at the auction. The circumstances that led to Hester and Tom being captured can't possibly have spread to the Anti-Traction League, they were immediately taken to the slave auction after being captured. Anna also instantly recognizes Hester when she sees her despite the fact that Hester was 8 years old the last time she would have seen her.
Suggested correction: Anna might have very well just been there to do anti-tractionist things, it was an auction made of towns after all a prime target to hit many options at once or hide bombs on for a bigger city to gobble up and go off later. Once she saw Hester her plans simply changed. As for how she recognized her, it is possible Anna had been tracking / keeping an eye on her. It wouldn't be impossible to ask around for a scar faced girl moving from town to town and might have gotten a pic somewhere.
These are all wild guesses that aren't confirmed by the film itself. They do not qualify as corrections.
Plot hole: How did Carolyn Fry get out of the cave in the canyon to confront Riddick at the Skiff? Riddick strained to roll the rock into the cave entrance, and he was a big, strong man from a position of good leverage. How did Carolyn and the other two push the rock out of the way so that Carolyn could get out? And, then, how did Carolyn mange to push the rock back into place? It was still there when she and Riddick came back from the Skiff to bring back the other two.
Plot hole: Batman finds at Belson's home a handwritten list of substances needed for a transplant. Why would Belson, a medical authority in the field that knows those things thoroughly, even write a list down? If it's for Freeze to procure him the material, why would it be at his house and not with him, and when did he even have time to be at home to do that, since he has been kidnapped by Freeze when he was driving on the outskirts of Gotham and taken to the oil rig? If he had time to go home, he at least would have changed clothes, he's still in the tuxedo he wore when he was kidnapped the night before.
Plot hole: Jenny steals Dr. "Sanchez's" badge by bumping into him so she can get into the lab, but she never did anything to return it. But Dr. "Sanchez" is still somehow able to walk into his lab without his badge. And even if he thought he left his badge behind in the lab for some reason and had someone let him in, he doesn't do anything to look for it, which would have alerted him to a security breach before seeing the scarab missing.
Plot hole: Rhona Mitra is told she can't fly into Scotland because it's a "no fly zone." But it's all part of the UK, and she's being sent in as part of a UK government operation. The only group enforcing the no fly zone would be the UK government, so they could send her in via whatever means they like.
Plot hole: Although the errand bird always insists on the postage and even asks for additional fees for more than twenty words, he never gets any payment from the assigning characters.
Plot hole: When we first see the reanimated Sparky, his head's sewed on. While that makes him look a bit like the traditional Frankenstein monster, it doesn't make a lot of sense - the original monster had stitches on its neck because it was made from multiple body parts, but it's not like they sawed the dog's head off after it died...
Suggested correction: Do we ever see how much damage the car did?
Plot hole: A Bug meteor knocks out the Roger Young's communications. She dodged it at sublight maneuvering speeds, indicating that it is moving fairly slowly. If it is so important that she warn Earth it's coming (which is how we know their comm was damaged), why doesn't she jump back to tell them or destroy it herself? Even if she has no capital ship weapons (she is a troop carrier), there is no indication that her faster jump drive is damaged or needs longer than they have to warn Earth to charge for a jump, or that she can't leave her patrol station, etc.
Plot hole: Wouldn't Taylor have suspected he was still on Earth, seeing as all the apes were speaking English?
Plot hole: At the bar shootout where everyone except Marlboro and Harley are murdered, the two jump through the window, over the fence, into the airport, and into an airplane luggage compartment. They would have been caught by security. The missing, and dead, airport worker would have been missed and searched for, the gunfire would have attracted attention, and the police would have been called. They never would have left the airport.
Plot hole: It is stated that the "specters" are actually made up of Bose-Einstein Condensate, and that they are so exceedingly cold, they instantly kill whoever they touch, presumably via shock. This is all good and well, except that if they are so cold that they could instantly kill a person, there should be physical signs of their exceedingly low temperature around them or at very least on their victims. If nothing else, at least some frost buildup around them when they stop for more than a few moments or discoloration on the skin of the dead.
Plot hole: The system providing oxygen can only be accessed by someone slim. Therefore John Goodman built the bunker with him unable to access the key facility that provides oxygen in his bunker. Yet he must have been able to go and get Britney when she went to that area?
Suggested correction: It's not a plot hole because he said in the film, the normal hatch to the air filtration was blocked by something that fell on top so they couldn't get through that way.
Plot hole: The use of massive explosives to separate a ship makes no sense as the explosion would send fragments at high velocity in every direction guaranteeing it would penetrate whatever ship is remaining. As we see in the final scene when the ship does blow apart, it is not a precise controlled detonation to sever connections but a total (and glamorous) explosion which makes no sense whatsoever.
Suggested correction: The explosions breach the outer hull, pulling the debris outward with the explosive decompression, the film shows the ring shaped explosions at both ends of the corridor. The debris wouldn't hit the lifeboat because it is heading in a different direction.