The Walt Disney characters are seen getting their costume heads prior to the parade. When the characters are seen on parade inside the tent, they are in different costumes to what they were wearing when they got the heads.
In one scene Buttons the clown is wrapping cloth tape around Holly's trapeze bar. He wraps it for about a third of its length then lays it down. When he lays it down it is clear that there is almost no tape left on the roll. When he picks it back up a short time later the bar is wrapped almost three quarters of the way and the roll of tape is much bigger.
When the view from the cab of the second section train is shown approaching the rear of the first section, the first section is parked on a right hand curve in the tracks. However, when the second section is shown colliding with the first section from the viewpoint of the middle of the first section as well as in some previous shots, it is obvious that the first section is parked on a left hand curve.
When Klaus is seen waving to stop the second section as the engine speeds towards him, the right Cylinder on the Locomotive are discharging steam. When Klaus' car is hit by the locomotive, there is no steam in sight. As a side note, the left Cylinder cock is not discharging steam, in fact both would very quickly alternate on and off.
Obvious split-screen background. It is known the production used detailed models for the trains in various scenes, and it is very obvious in the scene where the first section stops at the flare, as the engineer and other crewmen seemingly jump out of thin air to land on the ground next to the train.
It's medically impossible to perform a blood transfusion by directly siphoning blood from one person to another through a tube, a procedure done here in that manner from Sebastian to Brad following the train wreck.
When Holly & Sebastian do tricks of balance, on a chair on their own trapeze bar, each character is on, Sebastian successfully throws his chair away and sits on the trapeze bar. As Holly throws her chair away, it shows as if she was able to grab on to the trapeze and not fall to the ground, just by grabbing the trapeze bar with one wrist and be able to hang on, uninjured, not even a wrist sprain. The way she falls also shows that there was a safety line used and hidden in post-production as she falls incorrectly. Additional fact: while Holly was setting up her chair, she mis-handled the chair and did not fall to the ground, below.