When all of the engines are talking about Spencer in the shed at the beginning of the movie, in an overhead shot, the creators reveal that they forgot the marsh pit by the turntable that Gordon fell into in Season 1 Episode 24: 'Gordon Takes a Dip."
When Hiro was first discovered, there were bushes and trees all around him. After that scene, the area was cleared out almost like a miniature valley for the rest of the movie.
The amount of jelly, leaves, twigs, and branches on Thomas change between every appearance before meeting Hiro.
Henry spoke to Hiro about his problem of needing special coal, and was upset over it. The creators forgot that in season 1, episode 18, when he first got the coal, he was happy and Thomas was jealous. Then in episode 19, he was taken off the special coal so his firebox can get upgraded. He does not use special coal anymore, period.
Kevin the crane has his crane wired on backwards. That is why things keep falling off of his crane arm.
When Gordon challenges Spencer to a race after Hiro and Thomas "make a run for it", it was revealed that Sir Topham Hat and the Duke & Dutchess were inside Gordon's express. If that were the case, they would have seen Hiro sitting on the tracks with Thomas. Yet, they didn't hear about Hiro until Thomas tells Sir Topham Hat at Knapford.
In the second scene of the engines at Napford Station, the overview showed Toby and Edward was part of the "pow wow", but when Spencer came along and talked to them, Toby and Edward was no longer there.