The trailer Cody is locked inside is shown to have a second layer of mesh in addition to the main bars, 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.
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.
In the scene where the eagle is trapped, Cody grabs onto the rope of the trap and Jake throws a rope around Cody's shoe to lift himself and Miss Bianca after him. As Cody tries to cut through all of the ropes, both of his feet are visible and there are no mice hanging from them, but when he arrives at the top of the cliff, Jake and Miss Bianca are there.
In one scene where Wilbur is being hospitalized, the doctor is seen in a green surgical outfit and cap, and is donning a glove. A couple of shots later, he is seen observing an X-ray from behind, and he is back in his normal white coat with no gloves or headgear. In the next shot, he is wearing surgical gear again.
When Cody is imprisoned with McLeach's animal captives, there is a shot of the Kangaroo and Koala Bear, in which the hook they later use to get the keys is visible, leaning against the wall. In the next shot of the same characters, the hook is gone, and then reappears later when it is used to get the keys.
In the scene where McLeach captures Marahute and Cody tries to rescue her he is shaken off by McLeach. When his foot is caught in a rope Cody hangs upside down and his shirt comes down almost to where it looks like its going to fall off. In the very next scene his shirt is perfectly normal and in the scene after that its back to the way it was at first.
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.
After Cody gets caught by Percival McLeach and fails to free his animal friends. His animal friends remain in their cages and chain collars are left behind there in McLeachs hideout. The animals left behind in cages include Red the kangaroo, Frank the lizard, Polly the platypus, Krebbs the koala bear. It's unknown if Cody, Bernard, Bianca, Jake stopped by McLeachs hideout to free the animals. Or if they go back to pick up Wilbur who's watching over the eagles eggs. Also the ending with Cody reuniting with his mom at his house is missing from the movie.
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.