When Whiff and Percy found Thomas, Bash, Dash, and Ferdinand, they were facing each other. But when they were heading back to Sodor, Whiff and Percy were facing away from Thomas, Bash, Dash, and Ferdinand.
When Thomas is breaking free from the freighter on his raft the running lights on the ship are reversed. A red light should be visible from the left/port wing and a green one from the right/starboard, not the other way round.
Even though he didn't have hands, Whiff was able to adjust his glasses.