I've just watched Miss Peregrine's Home for Peculiar Children and at the end, they say that Miss Peregrine cannot open another loop while she is injured. However, I rewatched the scenes where she appears and I cannot find when that happens.
Barron coerces her to go into the cage in bird form, and the next time we see the bird is with the other birds in Barron's hideout. Jake frees her, she attacks Barron, and leaves flying through an opening in the roof. Nobody even tries to hurt her. Did she get hurt off-screen, or is there an extended version or something?