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Plot hole: Throughout the film, Sodor seems to be devoid of humans besides Bertie's driver and the live-action humans. Also, the engines with the exception of Lady do not have crews.

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Season 1 generally

Plot hole: James appears in every episode before his introduction in "Thomas and the Breakdown Train." Also, James is supposed to be black, because at the end of the episode, James is told he will get a different coat of paint. (He is also black in the book).

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Plot hole: Several of the giant organisms were too big to fit through entrances. Such as the spider entering the basement, and the ducks entering the dance hall.

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Wonky Whistle - S15-E17

Plot hole: Thomas or his crew should've realised that the whistle was "wonky" the first time it was blown.

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Respect for Gordon - S9-E6

Plot hole: When Gordon crashes into the goods train, it is not being pulled by an engine. So why is it just sitting on the mainline and not on a siding?

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Middle Engine - S6-E14

Plot hole: Percy was blamed for being on the coal tipper when it was Arry, Bert, and Henry's fault. None of the three got consequences. Also, why would the workmen tether Percy or even activate the coal tipper when they knew he was an engine?

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