Many people have pointed out that there are more than a few inaccuracies relating to the Owl's biology. However, as of the third book, the series is stated to take place after Humans have gone extinct. We're never told how long it's been, but humans were extinct for a very long time; long enough, perhaps, for Owls to evolve to the way they are in the book.
Fridge Horror
It's heavily implied that the Others (i.e. humans) are long gone/extinct. All that remains of The Others' civilization are ruins and artifacts.
According to Word of God, the story's setting is indeed an After the End where humans are extinct, and St. Aggie's and other works of architecture left behind by the extinct Others.
The moonblinking done to owlets at St. Aggie's, and later when the Pure Ones infiltrate St. Aggie's with flecks.
Ginger torturing an animal, which is cruel and forbidden because to do it disrespects the life prey gives. Not to mention her brainwashing Eglantine to be a spy for the Pure Ones and to believe her parents are still alive and living with Soren and Kludd in their old home. If that weren't bad enough Nyra is pretending to be Eglantine and Soren's mother.
Nyra kills Coryn's poor friend, the Sooty named Phillip, by ripping out his heart. It was what Coryn was supposed to do to prove his loyalty as a Pure One. Phillip's last words were telling Coryn to run. Nyra only allowed Coryn to be close friends with Phillip so he'd have someone to kill for his initiation. Kludd tossed chick Soren out of the nest to become a Pure One, something Coryn saw in the flames with his Firesight.
Nyra forcing the Blacksmith of Silverveil into her forge is downright nightmarish and tragic. Nyra even says that since Ga'Hoole owls cook their meat that they should serve the Blacksmith to the owls at the Tree! As if we didn't know how bloodthirsty Nyra was already.
If the Pure Ones' talon salute isn't supposed to be a Nazi salute, I don't know what it is.
Fridge Logic
A skunk attempts to spray Coryn in book eight, but he's safe due to the height he's flying at. In reality, owls have next to no sense of smell and are unbothered by skunk spray - hence they are the primary predators of skunks. note The owls' tendency to take in scents was hand waved in later books as simply a feature of owls in the books' universe.
