Revealing mistakes: When the elves are helping the children out of Santa's sack the elves move and motion as if they are getting the "know it all" out of the sack, but there is no boy between them.
Miscellaneous: The first time the boy goes downstairs on Christmas eve there is a red snowman skirt on the tree. Then on Christmas morning, as the train is going around the tree the skirt on the tree is yellow kind of color and has bells on it.
Revealing mistakes: When the elves are first seen, there is an elf that is moving (translating) left to right in front of the train with all the others, but the elf's body is rigid and lifeless, like a toy being slid across the floor. Possibly the computer animation for moving the elf from left to right was correct, but the algorithm for animating the body motion (walking, swinging arms, etc.) was stopped.
Continuity: When hero boy is riding on skis with hobo on roof of train, the camera angle pans several times. At one point, the view is from the front of the train, showing the engine and the two fellows are on the third car, with two cars between them and the engine. Subsequent pans show them jumping at least three more times, and traveling on more than just two cars.
Continuity: Throughout the movie, the number of cars on the train changes, from just three, to as many as eleven plus. This is most obvious when the hobo and Boy are skiing on the roofs of the cars.
Errors in geography: The moment the train crosses the Arctic Circle at 66 degrees and 33 minutes North it arrives at the "North Pole" which is located an additional 23.45 degrees north (A fairly lengthy distance).
Factual errors: In the cab scenes, the controls are backwards. The Throttle should be pulled back to increase speed. Pushing it forward would apply no power to the drivers. Also the Brake handle is pushed away to apply the brakes, it should be pulled toward the engineer to apply them.
Continuity: When the Hero Girl's ticket has blown outside the train and comes back in and rests on an air intake, in the following shots it disappears and reappears.
Revealing mistakes: The stoker uses his hair pin to replace the missing pin on the throttle. However, when the pin is in place, the engineer pulls back on the throttle as though it were the brake (evident because the train starts breaking instantly giving no time to actually apply it).
Continuity: When Hero Boy jumps into the car with coal and then gets out of it, the coal doesn't leave any marks or stains on his body or clothes.
Audio/visual unsynchronized: When the train runs into the caribou, the noise they are making is actually that of elk.
Factual errors: Know-It-All states that the train is a Baldwin 2-8-4 locomotive built in 1931. The Polar Express was modeled from plans of Pere Marquette 1225 which is a 2-8-4 type built by Lima Locomotive Works in 1941.
Incorrectly regarded as goofs: When the Conductor takes the Girl who has lost her ticket to the engine, they walk along the tops of the coaches rather than simply remaining inside. In the real world, there would be absolutely no reason for them to do so, but this being a fantasy film, the rules of the real world don't apply.