Audio problem: At the beginning of the episode, Gordon has Edward's whistle sound.
Continuity mistake: The children waving at Toby disappear after Toby puffs under the bridge.
Continuity mistake: Alicia Botti was annoyed by Toby's appearance. But in "Thomas, Percy, and the Squeak", she thought Percy being dirty was the proper appearance of a steam engine.
Answer: He was in the water.