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.
When Thomas first starts off again along the magic railway tunnel after backing up to retrieve the missing sixth coal-wagon, there is clearly nothing in tow behind him; the coal-car only shows up hooked to Thomas in the next, "from behind", shot.
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.
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.
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!"