
Plot hole: Al Simmons' reasoning for wanting to quit A-6 is because he learns his rocket attack in his assassination mission in the beginning of the film yielded civilian casualties. This makes no sense, as he blatantly gunned down several innocent men in the air control tower just moments before.

Plot hole: When Jim is shown what he has to pay for the damages Herbie did to Mr. Wu's shop he says he has no money. First off if he had no money how in the world was he able to put down any money on the red sports car he had just purchased that night? Secondly, what happened to the prize money from all the races he was winning from the previous few months?

Plot hole: The Chinese army displays a great variety of (often anachronistic) weapons and they spent considerable resources arming and reinforcing the Great Wall to challenge the beasts who have been plaguing their land every 60 years for thousands of years. but despite having records of magnets being effective against them, with magnets being well known to them for centuries (early magnetic compasses were available in the IV century BC, and the movie is set in the XI century) they made no use of that at all.

Plot hole: The Mummy would not know where to crash the plane in England to retrieve the dagger from the Abbey as this was placed there thousands of years after her imprisonment. If she did know it was there using her powers she would know that the stone was missing, but she didn't.
Suggested correction: Ahmanet did know where to crash the plane. She had the ability of sensing the dagger. Jenny even points out to Nick that Ahmanet knew where to find it. Ahmanet's powers are not fully explained but, since she could sense the dagger, she probably thought the stone was still with it but didn't know until she tried to stab Nick. Later, when the Prodigium agents find the stone, Ahmanet could not only sense it but, told Jenny it was found.

Plot hole: When Sully and Mike are talking in the toilets, during Boo and Sully's Hide and Seek game, Boo comes running in screaming and upset because she's just seen Randall, and he's not too far behind since all three can hear him talking offscreen to the CDA before entering the toilets, but how did Boo get to Sully faster than Randall without him seeing her, and how did Randall not hear her screams since they're all in the changing rooms which have an echo?

Plot hole: In one of the late scenes Logan is interrogated by the mainframe computer, and is guarded by two other sandmen. No one in the city is allowed to be over thirty years of age, yet the guards are at least in their late 30s or early 40s.
Suggested correction: How do we know how old they are? Just because someone may look like they're in their 40s doesn't mean they are. I have several friends and coworkers who look older than their actual age.
I also thought the guards looked old. Yes, maybe they were 29 but since they had a minimal role, it wouldn't have been difficult to go with actors that actually looked like they were in their 20s.

Plot hole: When the chipmunks finally release their first song, there is a montage showing the chipmunks rising musical success. In one shot we see a marquee promoting "The Chipmunks Premiere CD Release", and on it is a picture of the chipmunks in the clothes Dave has made them (note Alvin in his 'A' jumper.) However, Dave doesn't actually make the chipmunks these clothes until further on in the film. (00:41:50)

Plot hole: Near the end of the movie, when Mr Potts finds out that he's going to be rich (Mr Scrumptious wants to buy his invention) and he rushes out to his car to go see Truly, he meets her en route and she's got her hair in an really elaborate style and has changed. But there is no way she could have possibly got to her house, found out that her father had gone to see Mr Potts to buy his invention, changed her outfit, done her hair like that and gone out to see Mr Potts in the short amount of time between Mr Potts and his children dropping her off, and Mr Potts and her meeting at the pond.

Plot hole: At the end, Jake utilizes multiple Loops to reach September 4th, 1943, the date from which Miss Peregrine's children impossibly entered another Loop set in the winter at the beginning of 2016. The closest date prior to this was in 1942, from when Jake waits for September 4th 1943 to arrive. However, having entered a Loop in 1942, he would have been unable to reach 1943 because he'd be stuck living the same day in 1942 over and over.
Suggested correction: Is it possible he left the loop while in 1942? The movie doesn't directly address that idea.
It does address this, actually. He'd have reentered the true time period upon exiting the loop. I suppose he could have prevented the local ymbryne who created the loop from resetting it, but if he did, he'd have doomed all those peculiars in the process. Not something Jake would do.
Several of the ymbrynes had been captured. It is very likely that the one who created that loop had been too, so the loop would have closed, and he could've lived in that time period.

Plot hole: The wolves seem to conveniently make an appearance to further the story, only to disappear in other parts. They are there for Belle's dad at the beginning and Belle when she tries to escape the castle initially. When Belle's dad leaves the castle after Belle takes his place and when Belle is freed to save her dad, they are not there.

Plot hole: The famous line "There can be only one" is uttered in every Highlander film. At the end of the original, Connor obtained the prize by killing the Kurgan and being the last one. However, in this film and others, you find out that there are still others around, such as Duncan, the woman who was Duncan's girlfriend in Endgame, the other immortals following Jacob in Endgame, and the ones that showed up in The Source. So, why did Connor obtain the prize? He still wasn't the last one.

Plot hole: The fact that Buddy placed the knife and note in the steering wheel of Jerry's car is unrealistic. Buddy first met Jerry in the bathroom after school started and Jerry hasn't gone outside of the school building to his car until this point later in the morning... so there's no way that Buddy could have known which car was Jerry's to pull this stunt.

Plot hole: April and Kenshin switch place in time as they were - by some extraordinary coincidence - holding the scepter "at the same time" (if the concept makes any sense) in the exact same pose, with a switch that takes several second of intense lightning storms and 'tornado weather' as one of the Turtles put it. Here there is the assumption that 4 priests would be around the scepter exactly at the same time, and when the Turtles do switch with Norinaga's elite soldiers instead they certainly were in completely different poses, far away enough to ride horses, who did not get spooked one bit by the lightnings and sudden winds but rode as if nothing happened.

Plot hole: If the Medjai are supposed to be the guardians against Imhotep and sworn to make sure he never comes back to life then why weren't they in possession of the key that opened everything in the first place?
Suggested correction: Because it got lost in the centuries that passed. It's possible they don't even know every step on how the mummy can return.