Rosie's Funfair Special - S12-E3
Audio problem: In the US version, Stepney says "Oh my!", but he doesn't sound shocked and his mouth doesn't match the words. In both US and UK versions: he blows his whistle multiple times, but it only emits steam once, and it sounds like Thomas' at a slightly higher pitch.
Gordon Takes a Shortcut - S12-E15
Audio problem: Stanley has a different whistle sound. His original whistle sound is essentially Thomas' at a lower pitch, but in this episode, it is Thomas' at a higher pitch.
Answer: Butch the breakdown truck must have pulled Gordon's tender all the way up the rails so the breakdown train can reach it and also Butch helped to get Gordon close to the winch.