In the scene where Grimble is fighting Nyra, he is attacked by two "Pure One" guards. After taking down the second guard, we see the ground where the two bodies should be, but are mysteriously not.
When Eglantine is carried away in a basket, Pete can be seen amid the crowd of onlookers, despite the fact that he is still as St. Aegolius at the time.
Several of the owl species featured in the film are not found in Australia, where it is set. This is because the original books were set in North America.
Owl talons are zygodactyl meaning there are two claws in the front and two in the back. The owls illustrated in the film have three in the front and one in the back.
Every time the gong at Ga'Hoole is struck, the sound of a bell is heard instead.
When the Guardians confront the armed bats, two models of Pete can be seen on screen at the same time.
In a couple of scenes taking place at the Great Tree, a resident Great Horned Owl appears to be donning Pure One dyes.