Early in the film when Hero Boy is in his room, his robe is seen on the bedpost closest to the bedroom door - when his parents visit the room, that bedpost is bare, then when he goes to see the train, the robe is there again (and he rips the pocket).
When the train passes by the wolves in the forest, it has at least 20 cars, but at the North Pole it only has 5.
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, and when they are on the ice tack.
Whenever the train is shown during the movie, all the cars' windows are fully lit from the inside. However, when the car containing the damaged and unwanted toys is shown in an interior shot, it is very dark and unlit.
The Hero Boy finds the Hero Girl's ticket on her seat. However, when she takes the cup of hot chocolate to the lonely boy in the next car, her ticket isn't where the Hero Boy found it.
The hero boy has to jump between cars because of the gap between them. In actuality there are metal plates between cars to cover the couplers and allow easy access. When the conductor and the hero girl move from car to car they simply walk across.
Whenever the engineer opens the throttle on the locomotive, he pushes it away from him, the further away he pushes it the faster the train will go. In reality, the engineer must pull the throttle lever towards him to accelerate while pushing it away from him closes the throttle valve.
As the train approaches Glacier Gulch, the sign says 179 degree grade. Actually, a vertical drop would be a 90 degree grade, so the sign should show something like 89 degree grade.
After the caribou begin to step away from the track, the conductor instructs the train's engineer, "All ahead... slow." "All ahead" is an instruction appropriate for a ship with multiple engines but not for a train pulled by a single locomotive.
At Herpolsheimer's, when Know-It-All says, "I want all of them!", the window on the car displays a reflection of a pile of presents, but those presents aren't seen in the actual store.
The controls, brakes, and other machinery on the train are set up in ways that don't make sense, but that's because it's pure fantasy. For that matter, many things that might normally be considered goofs can be explained by the fact that this movie is about a magic train to the north pole to visit Santa. The normal rules of the world do not apply to this movie.
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.
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). This is not important, as the place can be called North Pole with poetic license, as it's close enough.
The Engineer is commanded by the Conductor on the ice using "Left full!" and "Right full!" in order to steer it toward the tracks. In reality and as can be seen when the ticket is blown under the engine, the drive wheels of the locomotive are connected by thick, solid axles, which though they can move forward and backward, would not allow the train to turn left and right like the Polar Express was able to do. However, the Hero Girl says that the train is magical, which could allow it to do things that a normal train would not.
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.
All the characters when they ring the bell hold it by the bell instead of the ribbons. The bell will not ring if this is done.
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.
When the elves are helping the children out of Santa's sack the elves move as if they are getting the "know it all" out of the sack, but there is no boy between them.
As the train is being pulled up the mountain with the track that curls around it tightly, just before the train enters the bridge that leads to the North Pole and as the Conductor is relating the story of the time he nearly fell off the train, the cars curve and bend to match the track as though they are made of rubber. This was done because the curve is much too tight for the cars to manage without scraping into the mountain.
When the boy pulls the robe from the bedpost, the robe is extremely poorly designed by the FX people. It is hanging on the post by the pocket? and when it rips, the physics of pulling it should have ripped the top of the pocket not the bottom. Also, the marbles in the pocket which spray out on to the floor from the pocket should never have been able to stay in the pocket because it was upset down. There is also no long sleeve arm on the robe when he pulls it.
The end credits list the position of "Mr. Hank's costumer" rather than "Hanks'" or "Hanks's".
When the train runs into the caribou, the noise they are making is actually that of elk.
Whilst the train is still reversing at and departing the North Pole, the conductor's announcement comes too early compared to the image. From what follows, clearly the announcement is in response to the train soon approaching 11344 Edbrooke rather than in response to its departure from the North Pole. It's a long journey after all.
At the start of the return journey, when the train is reversing itself by circling counterclockwise around the Christmas tree, tracks are visible only outside the North Pole Square but not inside. Should there be really no tracks in the square, the train would head down some undesirable directions and crash into stuff / elves. Moreover, much earlier should the elves have cleared the tracks as the train passes through the square.
When the Hobo is talking to the Hero Boy about belief in Santa Claus, he tells him that he doesn't want to be led up the "primrose path," as if meaning that he does not want to be deceived. Being led up the "primrose path" denotes a life of luxury, while being led up the "garden path" suggests being purposely led astray.
When Hero Boy applies the brakes, the train comes to a stop even though he didn't touch the throttle. Later, when the throttle breaks, the engineers don't think to use the brakes to stop the train.