Iconic Character, Forgotten Title: Commonly called "Thomas the Tank Engine" after the show became popular. It doesn't help the merchandising between the two products sometimes interchanges and some versions of the original novels are even released officially with the Thomas moniker.
Nightmare Fuel: Many of the books about scrapping, even Edward the Blue Engine, seem to traumatize steam lovers.
Ron the Death Eater: An example for a character that didn't appear much, 98462 was stated by Reverend Awdry to have been sent away because he was rude and nasty. In Trainz-based Thomas fan videos, 98462 is often derailed into a psychopathic bomber.
Villain Decay / Time Marches On: In the 1960s, books like Stepney the Bluebell Engine and Enterprising Engines dealt with the subject of Modernisation; in the former, Percy goes as far as to demonize controllers on the mainland, only for Awdry to set the record straight in the foreword by saying the British Railways officials are not cruel, and are in fact supportive of the preservation movement. In James and the Diesel Engines, published in 1984, a visiting diesel notes that on BR, "steam engines are kept in their proper places, and aren't allowed out on the mainline without special permission." (referring to the red tape surrounding steam-hauled railtours that has only become stricter as the years passed, due to evolving railway safety standards and environmental laws.)