Plot hole: The whole movie plot relies on a very unlikely assumption: that the ex-husband would not visit Kidman at her mental institution where he put her in, nor call for any news at all, for four whole years... Even though divorced, they still share a common child! And what about the parents / siblings / extended family/ friends of Kidman? Would they also never visit for four whole years? If any one of them had, then they would have known the (fake) ex-husband had taken her out and would have called the real husband to get news. Then Kidman would have been reported as kidnapped.
Plot hole: When Vlad enters Mehmed's tent, the entire floor is covered in silver coins and Mehmed remarks on Vlad's weakness to it. There's no way that Mehmed could have known about Vlad being a vampire or about his weakness to silver, as Vlad had killed every Turk after becoming a vampire, so nobody would be alive to tell him. Even the Turk found on the battlefield in the morning lived long enough only to deliver Vlad's message, but died immediately after that.
Plot hole: When April O'Neil calls Vernon Fenwick (drives the channel 6 van), he answers his phone and immediately says "O'Neil". When the scene cuts back to O'Neil, we see she called from a payphone. Fenwick would have no way to know it was her calling.
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.
Plot hole: SPOILER: When Amy comes back, doctors would have checked her non-existent head wound from the "abduction", from where she supposedly lost that much blood. That would and should have revealed all of Amy's lies.
Plot hole: There is no logical reason to switch off the Bombe at midnight when the codes change. Firstly, Turing's proving the concept of automated code breaking, so even if it only finds the right settings days or weeks later, the experiment is worth doing, then you can work out how to speed it up to be operationally useful. Secondly, even in steady state operation, cracking "yesterday's" settings (and thus intercepted signals) is still going to be pretty useful in most cases. Threatening to smash the Bombe up at midnight is good stuff to add some movie tension but, in reality, it's nonsense.
Plot hole: Towards the end the Rich Purgers call for reinforcements, and Shane, Leo, Eva and Cali are hiding behind a wall. A guy somehow opens a door in front of them (without being seen by the three facing him), exposes himself and shoots only Shane, numerous times, to cause his death. He should have been spotted by the people looking in his direction. Also, if he was that well hidden he could have simply sprayed the entire group. He unloaded 5 or 6 shots to Shane's chest...when he could have taken them all out.
Plot hole: Thomas and Minho decide they are going to go check out Section 7 after they find the creature they killed was from there. But Minho states that when the maze changes, a different section is open every night. Section 7 was open the previous night but they decide the next day that they are going to go to Section 7 to check it out. Then when they get there, Minho is surprised to find Section 7 open and states that it's not supposed to be open for another week...but that's why they went there in the first place.
Plot hole: Towards the end of the "The Hard Goodbye" segment from the first film after Marv has killed Cardinal Roark, a newspaper clipping shows that the Cardinal's brother Senator Roark was decrying the atrocity. However, at the very end of this movie, Nancy kills Senator Roark with Marv's assistance. Since Marv was captured and imprisoned immediately after he killed Cardinal Roark, that means that the killing of Senator Roark had to have occurred before "The Hard Goodbye", which means Senator Roark should not have been alive to decry his own brother's murder.
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: After everyone flees the family home, as Optimus is escaping he is pursued by a helicopter. He is driving down a road in a straight line. He never deviates. Yet the helicopter misses him every time, only narrowly hitting him on the side.
Plot hole: When April and her friends are trying to get to town, the road is blocked by a huge tree. Yet later in the movie, the police arrive at the cabin they are staying in. How did they get there since the road is completely blocked off and there's only one way in and one way out?