Revealing mistake: In a close up of Percy's driver, he is in Henry's cab.
Revealing mistake: When Percy is at the "backing" signal, his cylinder is sagging.
Other mistake: The Breakdown Train to the left, in the opening scene, is derailed.
The Runaway - S2-E10
Audio problem: When Thomas is tired and approaching the station, he is moving pretty slow, but the sound of Thomas' wheels moving is like he's going pretty fast.
The Runaway - S2-E10
Visible crew/equipment: When Harold is flying, in one shot, a stage light is reflected off his blades.
The Runaway - S2-E10
Revealing mistake: When Thomas' fireman is ill, you can see a brief flash of red outside, meaning it's James. (Note: same footage from Old Iron).
The Runaway - S2-E10
Visible crew/equipment: When Thomas leaves the station, a tripod is reflected off him.
The Runaway - S2-E10
Revealing mistake: When Duck comes to Terence's field, the end of the track leads right into the bushes right behind duck.
The Runaway - S2-E10
Revealing mistake: When Duck is happy at the beginning, the breakdown train's buffer on the right is broken.
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.
Visible crew/equipment: When Diesel is on the turntable, camera equipment is reflected in the windows for several moments. (00:02:00 - 00:10:00)
Plot hole: When Duck and Diesel leave the shed, Diesel follows Duck instantly, but the tracks they are on both lead to the turntable. As they are on different tracks to each other, it would be impossible for Diesel to follow Duck that quickly as the turntable could only be set to one track at a time.
Revealing mistake: When Duck goes off to fetch Gordon's coaches following his chat with Diesel, the device beneath the tracks used to produce steam continues to smoke long after Duck has left.
Revealing mistake: Most of the engines' eyes are wonky when Diesel says their names and their eyes are wonky in a few shots of them.
Dirty Work - S2-E13
Visible crew/equipment: When Duck bumps a truck when the Troublesome Trucks are singing, "Pop Goes the Diesel", you can see a string pulling the truck.
Visible crew/equipment: When Duck is being pulled out by Thomas, from the shot inside the barber shop, a camera and other studio equipment is visible behind Duck.
Thomas Comes to Breakfast - S2-E18
Other mistake: The narrator said Thomas was feeling conceited, but Thomas had his sad face mask on instead.
Visible crew/equipment: When Bill and Ben are shunting, we can see hands. (00:02:00 - 00:10:00)
Character mistake: The driver said that Bill and Ben's names and numbers would be taken away, but the twins do not have numbers.
Visible crew/equipment: In the restored version, when Bill and Ben leave Brendam Docks, the twins do not disappear. They just stop right at the top of the screen. The end of the set can be seen in a still from the episode: also, two hands can be seen pulling them backwards with string.