The scene where Sir Topham Hatt tells Thomas he can't take part in the Shunting Challenge due to his accident, and that Percy has to take his place. Sir Topham looks legitimately heartbroken during this scene, like a parent telling his ill child that he can't come on vacation with the rest of the family. It doesn't help that Percy is worried about competing, and Ashima coming in to say goodbye before they all leave for the Mainland. The scene ends with Thomas alone at the Steamworks looking miserable and heartbroken.
The end when Thomas wants to say goodbye to Ashima and can't find her anywhere, amusing she already left.