I guess the use of 'fit in' here is natural, this line being part of a movie and all that.
Miss Peregrine: [to Jacob] Because our abilities don't fit in the outside world we live in places like this, where no one can find us.
This is an interesting, good question. Some people claim that "fit in" is a two word verb. This can be supported with sentences like this: He doesn't fit in.
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