Plot hole: When Abby and her kids are abducted, the sheriff is sitting right outside her house and sees this happening. Yet the video didn't record. Well the sheriff saw it all with his own eyes so why wouldn't his testimony hold up? The tape actually shows the UFO so there's proof right there. (01:08:55)
Plot hole: When Saxby tells Blofeld to watch Peter Franks on the CCTV, Blofeld would have recognised him as James Bond. Why does Blofeld keep quiet about it? What possible use could he have for catching, rather than killing, Bond? (00:38:34)
Plot hole: While a tracker can certainly make it so that Junior knows where Brogan is at a given moment, it is impossible for Junior to know where exactly the plane is going to land and be lying in wait, with Brogan walking right past him. Junior would have to be well ahead of the plane in order to do that, and know exactly what direction Brogan would walk to cut him off and ambush him.
Plot hole: Captain Bosch and AJ steal George Cooper's photos, but not the negatives. George Cooper discovers the photos are missing, and could have just recreated the pictures from the negatives. He is looking for who took his pictures later. (00:37:30 - 00:53:00)
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: 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: 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.