In the beginning of the movie, Balto's eyes are pale yellow. When he wakes up from the second dream, his eyes are white. After he hops off the boat, when he gets close to Jenna (after he runs with the puppies), his eyes are pale yellow again.
(at around 20 mins) On the boat, when Balto is telling Aleu of her wolf heritage and the shot moves to the wall when Aleu says "My grandmother was a wild animal?", her tail is curled, then she puts it down. But on the wall, Aleu's shadow clearly shows that her tail is still curled.
Aleu has four toes on each paw, but as a puppy, she only has three toes on each paw. Also, on the boat before she jumps off and runs away, she has three toes on each paw.
(at around 5 mins) In the beginning of the movie, when Balto checks on Jenna, he opens the door, and you see 3/4 of him. In the next shot, you see only half of him.
(at around 1h 10 mins) When Aleu starts her howl goodbye to Balto, you can clearly see that she isn't holding her left front leg in the air.
Wolf packs are not lead by unrelated wolf-dogs.
(at around 11 mins) When the puppies, who are eight weeks old, are being adopted, all their ears are up. At that age, their ears should still be down.
Throughout the movie, Jenna is missing the copper (Red and White) Husky's characteristic "snow nose" and the pink stripe it acquires in cold weather.
Balto and Jenna both have brown eyes, yet a couple of the puppies (including Aleu) have blue eyes. Blue-eyed offspring from brown-eyed parents is impossible. If a brown-eyed dog mates with another brown-eyed dog, all the puppies should have brown eyes, not some with blue eyes and the others with brown eyes in the same litter.
The wolverines are depicted with large, rodent-like incisors. Wolverines are carnivores, meaning they have small incisors between large canines.
(at around 1h 3 mins) In one scene, a wolf says "The old one spoke the truth about Balto". Although Balto's name was never directly heard from any character, it might have been said by Nava when the camera wasn't focused on him.
(at around 55 mins) When the other wolves have left, Balto and Aleu are by themselves, and there are clearly shadows under them. When the raven flies by, it has no shadow on the ground.
When Sumac is approaching Balto and Aleu on the cliff by the water, a shot from almost underneath him shows that the toes on his front paw are not drawn in, and his back paw has the toes and their pad, and the bigger pad is missing. Also, Yak's toes are not drawn in on one of his paws. These goofs happen for just a brief second.
When a wide shot shows Nava on the cliff and all the wolves gathered below, you can see that some of their eyes are just black circles, while others are pale yellow circles.
At some points of the movie, characters do not leave pawprints behind.
At some points of the movie, some of the wolf clan members (excluding Niju, Nuk, Yak, Sumac, and Nava) do not have mouth outlines.
Throughout most of the beginning of the movie, the raven's beak does not move whenever it caws. When Balto is by the river talking to the raven, the raven caws several times but it's beak doesn't move, yet in a later scene, when it caws, its beak moves.
(at around 3 mins) When Balto and Boris are at the totem pole with the raven at the top, Boris points out the raven and wolf, Balto says "Calm down, Boris. There's also a fox, a wolverine", his mouth doesn't move at all when he says "wolverine".
(at around 21 mins) When Aleu is running away, Balto says "Aleu? Aleu, come back!" but his mouth doesn't move while he's saying it.
(at around 1h 7 mins) Near the end of the movie, Aleu says "Nava won't be able to make the swim.", but her mouth stops moving before "swim" is heard.
(at around 26 mins) After Jenna says "You mean you told her about being part...?", Balto says "Yes" as he turns his head, but his mouth doesn't move when he says it.
All of Balto and Jenna's pups, not only Aleu, are second-generation wolf-dogs, but the humans do not seem to care about this, as only Aleu looks like a wolf. In real life, the trouble with wolf-dogs is caused by people ignoring their needs and treating them like pure dogs. So in this case, the other pups would be more dangerous.