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 finds Percy, he is behind him; but later when they arrive at the Steamworks, Thomas is in front. The same thing happens with Edward.
Factual error: When Spencer brakes after he hears Percy whistle, his bogey wheels spark, but they do not have brakes.
Factual error: Black smoke comes out of Henry's cylinders, when it should only be coming out of his funnel.
Continuity mistake: Gordon's Hill is much taller and steeper than it usually is. Also, when Belle reaches the other side of the hill, the tracks on the viewer's left disappear.
Continuity mistake: When Thomas passes Gordon, Butch's magnet is attached to Thomas. In the next shot of Thomas, it isn't. And in the shot after that, the magnet is attached again.
Audio problem: When Thomas and Butch deliver Rosie's wheel, her whistle sound is at a higher pitch.
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.
Audio problem: When Den and Dart bully Flynn, their voices are swapped.
Continuity mistake: When Flynn sprays Edward, the water goes over Edward, but somehow his driver gets wet. And when Flynn sprays Gordon, the water is seen hitting the platform and Gordon's tender. Later, the water is seen hitting one of the coaches.
Factual error: In the U.K. narration, when Flynn sees Gordon, the narrator says "Flynn steamed in to a stop." but Flynn isn't steam powered. This mistake is fixed in the U.S. narration.
Answer: He was in the water.