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.
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".
Before Aleu says that Nava won't be able to make the swim, look at the top of her left leg. There is a triangle-shaped patch. In this long continuous shot, the patch disappears when Aleu starts speaking.
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.
When all the wolves are getting ready to leave, Nava, who is near the edge of the cliff, points out the ice floes coming together to form a bridge. A couple of shots later, the bridge is seen forming again.
When all the wolves are getting ready to leave, Nava, who is near the edge of the cliff, points out the ice floes coming together to form a bridge, when before there was clearly empty ocean a few shots ago.
When the puppies are being adopted and it's down to Aleu and four red-and-white puppies, a human takes one, leaving Aleu and 3 red-and-white puppies, but after that, when a shot shows the puppies jumping, it shows that there are 4 red-and-white puppies, but Aleu is nowhere to be seen.
At some points of the movie, Aleu's ears are the same color as her body and not darkened. One such scene is when Balto is pulling Aleu onto the cliff using a tree branch. Look carefully at Aleu's right ear. In this long continuous shot, it is darkened, then suddenly, it is not darkened. The next shot then shows Aleu with both ears darkened again.
After Niju says "You're outnumbered, half-breed.", a wide shot shows Niju and the other wolves advancing toward Balto. Look carefully at Niju's upper jaw. In this shot and the next, his upper jaw is black, when it should be gray. In the same shot, Balto says "Nava's right, Aleu." and Niju comes on-screen briefly, and his upper jaw is gray again. Also, Niju is missing the eyepatches, which are taken up by his eyes. After Niju turns around, his face is normal again.
During the song "The Grand Design", Niju tricks one of the wolves with a bone, and they all jump into a pile. When the camera zooms out and shows the pile, the number of wolves in the pile is inconsistent with how many wolves there were before.
When Balto is talking to Jenna about Aleu running away, there is a telephone pole with no wires visible. Two shots later, there are clearly wires on it. The whole scene ends up with all of the telephone poles having clearly no wires whatsoever.
The ratio of red-and-white puppies to brown-and-white puppies changes during the shots that show the puppies running. It changes from one brown-and-white puppy and four red-and-white puppies to two brown-and-white puppies and three red-and-white puppies, then back to one brown-and white puppy and four red-and-white puppies again.
When Aleu is howling in the crate and Jenna tells her to stop, a brown-and-white puppy is covering his ears. His head is brown with a white muzzle. In the next shot, however, when he jumps onto Aleu, his head pattern is clearly different than in the previous shot.
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.
When the ice floes come together for the second time, the shapes of the floes are clearly different than when the floes were shown the first time. Also, their size and position change. When the floes are first coming together, the "bridge" is two or three floes wide, but at the end of the movie, the "bridge" is just one floe wide, and the floes are noticeably bigger than before.
When Sumac, Nuk and Yak (standing in that order, looking away from the wave) are by the edge of the spit of rock, they get drenched by a wave. Afterward, in the next shot, Yak is now on the left, and Sumac is now on the right, and they are facing the ocean. There is no way they could have changed sides and turned around that quickly.
In the cave, when Aleu says "I'm not a wolf." to Muru, she steps in a small puddle. In the very next shot, neither one of her paws is in the puddle. Also, when she steps in the puddle, the tan "sock" is clearly missing from her leg.
After Aleu says "I am Aleu, daughter of Balto and Jenna, who happens to be a pure-bred Husky," she says "Who are you?" to Muru and growls. In this shot, Aleu's ears are the same color as her body, and not filled in. This is corrected in the next shot.
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. But in the next shot we see of Aleu, her tail is down.
When the puppies are being adopted and it's down to Aleu and one red-and-white puppy, and Aleu and the puppy jump onto the edge of the crate, they are on the left side. When the human picks up the puppy, they are now on the right side. The following shot with Aleu waving goodbye shows her on the left again.
During one of Balto's dreams, when he's looking at the house with the light streaming out the door, he turns his head toward it. His ears are the same color as his body, and not darkened like they should be.
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.
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 Balto is playing with the puppies, and he rolls onto his back, the stripe on one of his legs continues down the leg and down the paw, when it shouldn't. The correct pattern is seen on Balto's other leg.
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.