Handy Pandy, the panda, is often seen in the fourth car of the birthday train with Perky the elephant before its fall into the trestle. But during the song "Nothing Can Stop Us Now," he's in the third car with Missy and Stretch.
During the song "Nothing Can Stop Us Now," there is a yellow bear-like toy in the back of the third car. It vanishes about a few minutes into the trek through the mountain and is never seen again for the remainder of the film.
When Control Tower shows Pete what he would be taking over the mountain, the stripes on his arms are lighter in color than they usually are.
During the song "Nothing Can Stop Us Now," Rollo the clown pulls out a bouquet of flowers from his hat. Chip the bird flies over to him and pulls out a red flower, but when he reaches Tillie, the flower has turned blue.
When Pete is about to be flagged down by Rollo, his mouth goes from black to white.
At the beginning of the film, Pete the freight train is assigned to take a printing press "over the mountain to the town." When he brings his delivery up to the toys, it goes into a flashback, and the background behind Pete and the crane is clearly a city, not a town.