Kodi has four toes on each paw, but in the flashback that shows him as a puppy, he only has three toes on each paw. Also, on the beach (after he's grown), when a shot from in front of him shows him running with Balto not far behind, he has four toes on his front paws, but only three on each back paw.
In the first movie, Balto's eyes are medium-dark yellow. In the second movie, his eyes are pale yellow, but in this movie, his eyes are back to medium-dark yellow, even during flashbacks from the second movie, when his eyes were pale yellow.
During Jenna's song "You Don't Have to Be a Hero", when a shot from underneath Balto shows a puddle with his and Jenna's reflections, his leg and chest are clearly missing the light gray coloring, clearly visible in his reflection. Also, it appears his left front leg in the reflection is not fully drawn.
When Balto (pulling Duke) is slipping down the icy cliff after the bridge has fallen, a shot shows that there are clearly no rocks or objects of any kind visible, yet two shots later, Balto puts his back paw on a rock that obviously wasn't there before.
When Balto is leading the team while following the plane, he looks back angrily at Ralph, only turning his head to the side. But in the close-up of his eyes, the reflection of Ralph makes it appear that Balto is looking at him straight on (or head-on), contradicting the previous shot.
When Balto is leading the team while following the plane, he looks back angrily at Ralph. We see that Kirby is behind Balto, but in the close-up of Balto's eyes, we see Ralph. We should see Kirby, not Ralph.
The flashback of Kodi and Balto playing when Kodi was a puppy showed Balto running with him as a scene from Balto: Wolf Quest. But in Balto: Wolf Quest, Balto was either talking to Jenna or playing with Aleu, but never ran with Kodi.
At one point in the movie (for just a brief second), when Kodi jumps while playing with Ralph, Kirby, and Dusty, when Kirby is in the puddle, Kodi's tail colors are switched around. The brown is on the bottom of his tail (where there's normally white) and the white on the top of his tail (where there's normally brown).
In the beginning of the movie, a couple shots after Kirby says "Zip it, Ralph! We would've been on time if you hadn't been dragging your butt the whole way!", in a close-up shot of Dusty, you can see the back part of Kodi and a small part of Ralph's face. Look at Kodi's tail. The white part is clearly missing, and it is only a longer version of his tail from when he was a pup.
Throughout the movie, the background of Balto's eyes is medium-dark yellow. But during Jenna's song "You Don't Have to Be a Hero", in the flashback, when saves young Kodi from falling, the background of his eyes is white.
In the scene where Boris goes to wake Balto up, Balto, in the wide shot, is shown with his head partially covered by a blanket with his nose sticking out, but in the next shot from under the blanket, his head is completely covered by the blanket.
At multiple points in the movie, a bush plane can be seen being used to carry mail. Bush planes in the 1920s were not used for deliveries, medicine, or mail. They were used for surveys and firefighting and were popularized after World War II. Before that, they were not a common sight. Also, bush planes were concentrated in Canada and weren't used commercially in Alaska until the 1940s.
At some points of the movie, such as when Balto is running with Kodi on the beach, characters run (and walk) through water (such as puddles or a small lake) without making a single splash. They step on TOP of the water, not IN it.