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.
Deliberate mistake: Due to the production order, Arthur can be seen at the quarry, but his introduction is 6 episodes later, in "The Spotless Record."
Deliberate mistake: When Thomas goes by the level crossing, a close up of Thomas is shown but it's the same footage from season 1, only flipped. Because of this, Thomas' number is mirrored.
Deliberate mistake: In the PBS airings in the U.S. of "Tuneful Toots" and "Duncan and the Old Mine", Rusty is referred to as a female rather than a male.
Thomas and the Sounds of Sodor - S16-E11
Deliberate mistake: When the engines are performing "The Sounds of Sodor", Emily, Thomas, Percy and Gordon have the correct whistle sounds but at a lower pitch. At one point, James has Emily/Henry's whistle sound, Mavis has her old "New Series" horn, and Thomas has James' whistle sound.