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.
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.
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.