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: Following Glen's death, Nancy tells her father to come across the street in 20 minutes to catch Freddy. She then goes to her house, checks and sets her alarm clock, and proceeds to rig the entire house with booby traps, including filling a light bulb with the contents of several shotgun shells, and has a heart-to-heart talk with her inebriated mom. When she gets back to her room to go to sleep, she checks her clock again. The time on the clock has advanced only ten minutes, not nearly long enough for everything she did.
Plot hole: When Jason is going next door to chase after Trish, he pulls Jimbo's body down from the doorway and begins walking towards Trish's cabin. He is seen walking by himself. However in the next scene, he throws Rob's body through the window. There was no time for him to go back and get the body. (01:17:15)
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: The whole film is basically told as a flashback from Rand Peltzer's point of view. Now he might be able to talk about things that Billy, his mom, or Kate might have told him, but he wouldn't have known about all the other the gremlins did to the rest of the town like killing Mrs. Deagle, the cops, or the gremlin in the mailbox.
Plot hole: If the underground women really believed that Einstein and Copernicus were female, they wouldn't laugh at the quote of Marie Curie.
Plot hole: When Arnie is driving the cop car and shooting at Conner and Reese, 5 or 6 inch holes from the gunfire are shown in the door right beside Connor. If the shell penetrated the steel door (which it could easily do - and was shown to do), there's nothing inside the door or on the other side of it to stop the bullet. Connor, and probably Reese, would've been ripped to shreds.
Plot hole: When the doctors are discussing the condition of Bowman's mother, a newspaper headline on the wall displays the pictures of both Bowman and Frank Poole. These pictures are actually still shots of the two actors from an earlier conversation they had with HAL in the previous film. Since Discovery has been dormant for nine years, how did Earth manage to use these particular shots for the newspaper?
Plot hole: Superman (or Kal-El) was a baby when his parents sent him away from Krypton before its destruction, and as Jor-El told his son in his first message he would have already been dead by then for thousands of Superman's years. Kara never existed during any of this yet so somehow she instantly recognizes him from the poster on the wall, even though she should have no idea who he is.
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 Buckaroo is speaking with the president via video call (with John Parker by Buckaroo's side), New Jersey is explaining the reason humans can't see the aliens from planet 10, is a result of bacteria produced by the aliens which is then absorbed by humans via their olfactory senses, affecting their cerebral cortex. If this is the case, why doesn't the president see John Parker in his true alien persona. He can't smell him through the television. (01:04:50 - 01:05:40)
Plot hole: When Sylvia gets grabbed in her apartment by the bad guys, she's screaming from the get-go and they are standing in front of the door all the time. So Moby should have heard her as he approached the door to ring the doorbell, the door obviously lets sound pass pretty well since he hears her muffled whimpers a few seconds later even being at distance. Somehow, her making noise becomes an issue only once the doorbell has rung and was a non-factor before. (00:43:50)
Plot hole: When Rachael/Ruby is attacked by Pluto in the rafters, Cass, being blind, is able to hear her cry out. When she does, Cass calls out to her by saying "Ruby." However it was a couple scenes later when Rachael tells everyone that she is really Ruby. Cass is surprised to hear this. Therefore, not knowing that Rachael was really Ruby, she should have called out "Rachael" instead of "Ruby" when she was attacked because she didn't know the truth by then.
Plot hole: Why would Madison take a bath in steaming hot water? The ocean water is warm or cold depending on the area of the ocean. So, it makes no sense as to why she does this.
Plot hole: Billy's not tall enough to impale Linnea Quigley on deer antlers.
Suggested correction: The movie blatantly shows Billy lifting her high enough above his head to impale her. It's literally right there in the scene. Additionally Linnea Quigley talks about the making of the scene in the documentary "In Search of Darkness Part II," and talks about the actor living her high above his head over and over while making the scene.