Continuity mistake: When the train arrives at the hero boy's house, the front engine is stopped directly in front of it. When the train is about to leave the front engine is stopped way far away in the distance. (00:09:30)
Factual error: When hero boy and girl and Billy are on the runaway car at the north pole, they crash into the stopper at the end of the tracks. They are flung backwards when in reality, due to inertia, they should have been flung forward into the guard rail.
Continuity mistake: During the scene when the Polar Express slides across the ice and the conductor is telling the train controllers to head for the tracks, the distance between the train and the tracks keeps changing.
Continuity mistake: When the boy runs out of his house, as the train is arriving, they make a point of showing his footprints in the snow along with his sliding leaving long marks. However, when they pan back it is his footprints that are gone.
Continuity mistake: After the Hot Chocolate scene, the little girl takes a cup to the boy in the last car. When she leaves her seat, there is no ticket there, but the boy sees that she left it behind.
Audio problem: When the elves are marching around, listen to the footstep sounds and watch their feet. A lot of times the noise and movements don't match. This is especially apparent when the five elves who have been taking wish calls go to the transporter.
Continuity mistake: Nearing the end of the scene where the boy and hobo are jumping from the roof of one passenger car to the next on skis, the camera shot changes from a close-up to a distant view. In this distant view you can plainly see that they have just two more passenger cars to jump onto before hitting the coal hopper. However, when the camera returns back to a close-up shot, they jump three passenger cars before the boy hits the coal hopper.
Continuity mistake: After the kids reach the North Pole and they line up outside of the train, Hero Boy and Girl are at the back of the line and we can see the other kids in front of them. In the next few shots, they discuss helping the Lonely Boy. When the camera comes back to the same point of view of the boy and girl being in line, the rest of the kids have disappeared behind them.
Other mistake: When they first arrive at the North Pole, one of the elves appears to be sliding along. His legs and arms are not moving, and his head is not bobbing up and down.
Revealing mistake: You can see Hero Boy putting the ticket in his pocket after getting it punched the second time, before finding his seat on the return journey. However, the ticket slowly evaporates in the air as he is about to put it into the pocket. His hand thus enters the pocket ticket-less.
Continuity mistake: Throughout the movie, the number of cars the train has changes. The scene where Hero Girl's ticket is surrounded by a pack of wolves shows the train having around 20 cars, but the scene where the train's on the ice shows it having 5.
Suggested correction: The entire journey is likely just a dream. There are many things in the movie that cannot happen in the "real" world, and the number of cars changing is just another aspect of the dreamlike nature of the trip.