Marahute's wings constantly change their span and shape when airborne.

When the delegates assemble in the Great Hall, it is first shown that Canada is sitting to the left of Morocco. In the next scene, Morocco is now sitting to the left of Iceland, and Canada has mysteriously vanished.

The notch in Jake's ear continually changes location throughout the film: sometimes it's in his left ear and sometimes in his right ear.

When Cody is running from McLeach and the lizard, Cody's backpack (which had been pulled off earlier in the scene) re-appears on his back for a moment, then disappears again.

The knife in the words "Satan's Ridge" on the wall map changes size and position.

When the French bug, Francois, first greets Bianca at the fancy restaurant, he calls her "Mademoiselle Bianca." After they finish their conversation, he says, "Allow me, Madame." In French, "Mademoiselle" is used for a single woman, and "Madame" for a married or widowed woman (or for very formal address). A native French speaker, as Francois is meant to be, would never use them interchangeably.

When Jake hijacks a snake to travel across the swamp he snaps the snake's eyelid. Snakes do not have eyelids.

This movie takes place in Australia and Marahute is said to be a rare golden eagle. Golden eagles are native to the Northern Hemisphere and Australia is in the Southern Hemisphere. Unless she was taken by illegal means and brought to Australia, she wouldn't naturally be found anywhere in Australia.

Jake is a Kangaroo Rat, but despite having "kangaroo" in the name, that species of rodent is only native to the western arid regions of North America, and would not be found in Australia.

In the scene where Marahute is carrying Cody through the sky, there is a moment where she starts tickling him with her claw, and at one frame, Cody's belly button disappears.

The trailer Cody is locked inside is shown to have a second layer of mesh in addition to the main bars. However, the mesh is not visible in some shots, including close-ups when it should be. In one scene when the mesh is visible Cody is shown putting his fingers through the bars but passing though the mesh as if it was not there.

As Marahute is pushing Cody along the river during their initial flight, just before the dive over the waterfall, there is a single frame where about half of the birds in the background appear as transparent outlines.

When Cody, Bianca, Jake and Marahute are trapped in a cage on the back of McLeach's truck, there is a single frame around 1:03:47 where the wire mesh texture on the left side of the cage becomes garbled.

When Bianca, Bernard, and Wilbur first enter Australia, the shadows on the Opera House disappear as they get closer.

The location of Washington, D.C. is placed incorrectly. It is shown somewhere around North Carolina.

Jake says birds of Wilbur's size cannot land at his airport, but the runway stairs do perfectly meet Wilbur's standing height.

McLeach tries to explain away the pit trap Cody fell into by claiming it is a hole Joanna dug to bury a dead squirrel. There are no squirrels in Australia.