Visible crew/equipment: When Bill and Ben go by a level crossing, the top of the set is visible.
Other mistake: The Breakdown Train to the left, in the opening scene, is derailed.
Wrong Road - S2-E22
Revealing mistake: Wires to power the lamps are very visible on Gordon's and Edward's buffers, and bulbs are also sticking out from both their lamps.
Visible crew/equipment: The reflection of a crew member's face is visible in the window of Edward's cab when his driver cheers him on.
Wrong Road - S2-E22
Character mistake: The narrator refers to the brake coach as the guard's van.
Percy Takes the Plunge - S2-E11
Deliberate mistake: When Percy is being loaded onto the flatbed, Diesel appears, but he is not introduced until "Pop Goes the Diesel" (episode after this). This is likely because "Pop Goes the Diesel" was produced before this episode.
Suggested correction: There is nothing in the show suggesting that the episodes are shown in chronological order.