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.
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.
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.
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.
Answer: He was in the water.