Factual error: A "wonky" whistle doesn't sound like a slide whistle, it should sound like a weakened version of the correct whistle mixed with the hissing sound of steam. A "wonky" whistle would also leak steam constantly instead of being blown like a normal whistle.
Continuity mistake: When Thomas goes back to Maithwaite, Flynn's railway wheels are not touching the rails, but his tires are.
Continuity mistake: After Thomas stops near the bridge, he does not have a Wonky Whistle.
Answer: He was in the water.