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Headcannon
All ymbrynes have to sleep in a nest, like it's the only way to sleep. And not a small nest, a human sized nest full of blankets and pillows, maybe made out of foam or softer material instead of wood. So, I imagine miss peregrine being too busy after the events of the movie to make a nest, no one knowing that she needs one, so she just doesn't sleep until she ends up passing out.
The children would have to call for another ymbryne to help them, the ymbrynes so confused as to why she doesn't have a nest that they and the children makes one for her.