In the first movie, Balto's eye scleras were medium-dark yellow. In the second movie, his scleras were white, but in this movie, they return back to medium-dark yellow, even during flashbacks from the second movie, when his eyes were white.
Stella changes from a pale mauve color to a pale white.
A couple of switches in Duke's plane change color. At one point in the movie, two switches are white, but one changes to red. Later, both are red.
The starting rotation direction of the propeller on Duke's plane changes throughout the movie.
The position of the post office continually changes throughout the movie.
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.
Boris is a snow goose appearing on screen sometimes wielding teeth. Geese or any other birds do not have any teeth in their beaks.
The resting angle of Balto's boat is steeper in exterior than in interior shots. This is intentional as the shot is re-orientated for the audience depicting the onscreen characters who adapted to living on such steep boat.
(at around 31 mins) During Jenna's song "You Don't Have To Be A Hero", when Balto walks away, no pawprints are left behind.
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.
At most points of the movie, characters do not leave foot- or paw-prints behind.
Throughout the movie, Balto is simply referred to as a dog, aside from the time when he attempts to decline the role as lead dog during the dog "meeting" and Kirby says "Let's do the call!" and howls.
The film is set in 1928, but in the scene that shows cars on the street, a couple of 1931 cars can be seen driving by.
(at around 52 mins) When Balto is talking to Kodi (with Kirby, Dusty, and Ralph) in the building, a modern-style electric box can be seen on the wall behind him.
(at around 38 mins) In the shot that shows the flight of Duke's plane on the map of Alaska, the location of White Mountain is inaccurate, being off its actual location by about 100 miles.