Revealing mistake: When Gordon puffs into the ditch his face looks wonky and wires are visibly attached to his cab.
James and the Trouble with Trees - S5-E5
Revealing mistake: In the end of the episode, you can see James doesn't have his face fitted on correctly, as the gap between it and his eyes appears to be exposed.
A Bad Day for Sir Handel - S4-E6
Revealing mistake: When Sir Handel derails, you can see a small rod sticking up out of the ground from the tracks.
Revealing mistake: When Thomas collects Rocky, the points are set against him. This also happens when Percy enters the siding.
Thomas Puts the Brakes On - S12-E17
Revealing mistake: When Stanley shunts Thomas into the yard, Thomas is eyeless.
Answer: He was in the water.