Other mistake: When the children arrive in Blackpool, Emma tells Jake that loop entrances can be anywhere and that "the one in London is in a subway tunnel", but on the map of all the loops they were viewing previously inside the boat, there was no marking of a loop in London.
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.
Continuity mistake: While Jake is inside the destroyed house, he watches Olive and Claire hiding from him. However, after he knocks himself out and wakes up, Claire isn't between the Peculiars near him.
Character mistake: Inside the loop Barron said the only thing he can't change/shape shift is his eyes but when Emma and Enoch rush in Barron is able to change his whole body, including his eyes.
Other mistake: When the Hollow is approaching Miss Peregrine by the shore, it doesn't cast a shadow when it's invisible. But as seen several other times in the movie, Hollows cast shadows when they are invisible.
