Generally, I think I liked this one just slightly less than the first. The only things I have to mention are a couple of complaints.
First, they were told Miss Peregrine had 2 days before she was stuck as a bird, so why did Jacob keep saying she had 3?
Second, They were so dumb sometimes in this one. It was so obvious that the loop they were looking for was in the crypt. I figured that out right away, but they "couldn't make heads or tails of it!" Then they thought Miss Peregrine's evil brother (who had already deceived them in a huge way once) was worth trusting, apparently, and believed him when he quickly surrendered to them. Come on, guys. That was too easy.
(show spoiler)
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