Plot hole: Throughout the entire movie, barns, houses, cars, 18-wheelers, etc. are demolished and lifted into the air like they were made of paper. And yet Jo and Bill pass through one tornado after another with nothing more than their hair getting messed up a little. You'd think the debris alone flying into their faces at 100 miles an hour would be enough to give them a few injuries.
Plot hole: During the scene where Merida gives her speech on "breaking tradition", her mother, as a bear, moves silently behind the majority of the crowd, so they don't see her. Fair enough. However, Merida and her father's clan are all looking in the same general direction (towards the crowd) while she's speaking - how does no one from Merida's clan see a bear moving at the back of the room?
Plot hole: Harry never notices that the name "Peter Pettigrew" appears on the Marauder's Map, right next to "Ronald Weasley." Way beyond a character mistake, as there's no way that wouldn't be cause for interest. If nothing else, Ron's brothers who had the map for years before giving it to Harry, would most certainly have wondered why their brother was sleeping with a person named Peter Pettigrew.
Plot hole: Christopher Columbus speaks Italian while the Huns supposedly speak their native language. Shouldn't Octavius and his Romans speak Latin? (00:34:50)
Plot hole: Simmons stands outside the 'The Monastery' at Petra (not to be confused with 'The Al Kazneh' at Petra where Indiana Jones and the Last Crusade was filmed) and looks at the horizon, and he is able to see the Air Force landing with Optimus by the pyramids. It then appears to take them mere minutes to drive over there. This is outright laughable, even accepting that they make the trip in an alien robot car. Petra and Cairo are separated by hundreds of miles of desert, not to mention Israel being between Egypt and Jordan.
Plot hole: This happens after Gabe has killed the guy in the cavern and is reaching for the radio. We hear Frank trying to reach them, so they must be on the same frequency. Then, Hal finds out that a bomb has been planted, grabs a radio from the bad guys and starts yelling for Gabe to get out of the cavern because of the bomb. Why didn't Frank hear any of this on his headset?
Plot hole: When Nick confronts the P.I. and yells "Why are you following me?", he looks inside the car and see the file with his picture on the front seat. The P.I. notices this and turns the file over. After Nick grabs his gun, the P.I. jumps out on the other side, raises his hands in the air and tells him someone hired him and runs off. As the P.I. runs off, Nick yells "Who hired you?" as he stands alone next to the car. He then waits a minute and walks off. If he really wanted to know more information, he could have taken the file that was right in front of him on the carseat. It makes no sense that he is desperate for information about the strange events that are going on, sees this file on him, and yet doesn't even pick it up or look at it. (00:59:55)
Plot hole: Why doesn't Reliant know that Khan is exiled here? The Federation is so terrified and opposed to genetic engineering that it's still illegal 300 years after Khan. So why is there no warning along with the data on the Ceti Alpha system? Kirk logged what happened with Khan and his solution of marooning him. Starships use nav data to navigate star systems. Ceti Alpha 6 exploded, yet the helmsman or computer never noticed that there is one less planet than there was when Kirk was there? There is no debris from the explosion? Ceti Alpha 5 is the exact same size and was conveniently blown into the exact same orbit as Ceti Alpha 6 used to have? So there is nothing whatsoever to make the crew even suspect that it's not 6? Enterprise would have to have scanned the planets in the system to know that one was habitable for Khan. Did Ceti Alpha 6's destruction somehow magically turn Ceti Alpha 5 into its exact duplicate? If Starfleet ships have been there to map after Ceti Alpha 6 exploded, none of them bothered to check on the exiles? Pretty callous for Starfleet, don't you think? With the technology and amounts of information available to Starfleet vessels, there is NO logical reason for the Reliant to think that this planet is Ceti Alpha 6. Finally, would the Federation be willing to test a device whose exact effects will be unknown on a planet so close to another inhabited one? (00:21:00)
Plot hole: The Toymaker throws that toy bird at the hippie version of himself. The toy goes through him because he is a hologram. Later, he pushes the soldier version of himself at the screen making it crack. How could he if the three others are holograms?
Plot hole: When the ship has turned on its side for the brief moment, it cuts to inside the ship where a hallway explodes, causing the ship to submerge. The only problem is the people are standing on the ceiling, but if the ship's on its side, they'd be on the wall, not ceiling.
Plot hole: Sarah turns up on the bridge to fight the Rev-9, we later learn that she is texted the location of where to be as when the terminators travel though time it causes a gravitational anomaly, and this is where she needs to be. The Rev-9 had been there ages killing Dani's dad etc, Sarah would have no idea to be on the bridge after the terminator has chased them though the town - she can't possibly know that location.
Plot hole: Radl and Steiner discuss the entire scheme to kidnap Churchill on the Alderney docks - in full view and hearing of a number of civilians (who shouldn't be there, pace another posting), including local fishermen. Though the Germans banned all fishing activities in the Channel islands including Alderney in 1941, they were well aware that there was a flow of information from the island to military authorities in the mainland. Why would they be so stupid as to discuss a top secret military mission in public? In reality, they wouldn't even discuss it in front of their own men.
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: In Night at the Museum 2, the parts of the tablet that are missing were attached to the gate to the underworld, which implies it was originally attached to that, and those parts were left behind when it was removed. But in this film we see the tablet getting found on the wall in Ahkmenrah's tomb, and the missing parts are left behind on the wall of the tomb.