For most of the movie, Clarabel is facing the wrong way.
When Mr. Conductor first sees and reaches for Rabbit's birch-bark note, the note is held in place by a wooden spring-clothespin, but then when Mr. C. retrieves the note just an instant later, the note is merely lying loose on top of the greenery.
When Mr. C. is being held by Pinchy, the hydraulic lines are just plain smooth rubber, but in the close-up of the tin-snips cutting one of the hoses, the lines are corrugated, like split-loom tubing.
Part of Pinchy's hydraulic system consists of a wide metal box-like structure with a group of three hoses attached to it. But when Mr. Conductor reaches to cut one of Pinchy's hoses with the tin-snips, there is just a narrow boxy housing with only one hose.
When Diesel-10 swings Mr. Conductor out over the river, the viaduct's keystone shakes loose and falls, then a few seconds later, two more large stones and a smaller one come loose and start to fall, also. But when Mr. Conductor then leans out over Pinchy's side and looks down at the river, the shot of his viewpoint shows all three large stones falling together in a tight group, as if they'd come loose all at once and gotten dropped together.
When Thomas leaves with the trucks of 'special coal', nobody couples them up to each other or him.
Diesel 10's weight should've sunk the barge when he fell on it.
The engines do not emit any steam when they whistle.
After Lily calls Thomas a 'really useful engine' the coal truck he is pulling disappears.
When Diesel 10 is chasing Thomas and Lady, he was on a different track from them. But when he comes to the hole at the viaduct, he is on the same track as Thomas and Lady.
When Diesel 10 was chasing Thomas and Lady, they (Thomas and Lady) were both smiling.
All of the Sodor locomotives seem to be able to run under their own power, yet Lady cannot.
The windmill blades would not go around, since they have no canvas on them to catch the wind.
The Steamworks appear in the film but they didn't exist until 2009. The crew didn't know about this.
Near the beginning of the movie, when several of the engines are greeting each, James says, "Hello, Thomas", but Thomas isn't present. Also, Thomas is heard saying, "Hello, James" in the same scene.
In the regular "Thomas and Friends" short stories, puffs of white steam are shown coming out of the engines' whistles when they blow them. But in this movie, no steam comes out when Thomas and his fellow locomotives blow their whistles.
As Toby quietly approaches the shed where the three diesels are conversing, wanting to eavesdrop on them, he is just moving slowly, and his smokestack is sending up only a couple of smoke-puffs per second. Yet the sound effects have him puffing rapidly, as if he's travelling at least 20 m.p.h.
In Junior's first scene, when Junior grabs his shell phone to answer Mr. Conductor's call, he removes his headphones, and the song "Summer Sunday" cuts off immediately, even though he didn't turn off his music player.
After Diesel 10 races past Gordon and Thomas, a pencil can be seen in the bushes on the right of the screen.
Shining Time's terrain includes mountains, valleys, and steep hills: southern Wisconsin's real-life surroundings don't match the environment in the film.
The Magic Railroad only has a single track running down it, so there is no way that Thomas and Lily could have passed the missing coal truck, and then "gone back" for it. Thomas would have had to come up on the truck with it sitting on the track in front of him, and then push it along ahead of him with his front buffers.
Toby tells his friends that he won't have to worry about being harmed by Diesel-10 because "I'm an old engine, and so he thinks I'm really useless". Yet when D-10 hears Toby's bell, he exclaims, "It's the old teapot! Smash him!"
The Island of Sodor is entirely devoid of humans in the film (aside from Lily, Mr. Conductor, C. Junior and Burnett Stone).