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.
Plot hole: On a certain date in 2016, Jake enters Peregrine's Loop on September 3rd, 1943 where her children relive the same day over and over and all non-peculiars are completely unaware of the Loop. When the Loop closes and it becomes September 4th, 1943, the children, without re-entering 2016, travel by steamliner to London and enter a Loop set in a date six months prior to the date from which Jake entered Peregrine's 1943 Loop. The trouble is, this Loop did not exist in 1943, so it should have been inaccessible to the children.