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Like Baba, Bio Rex, and Octoman, Pico isn't a villian.
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In the games, Roger only has those three red marks on the left side of his head.
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Roger has 3 marks on BOTH sides of his head.
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When they had an x-ray of Jody on the screen it shows robotic parts on her neck, arm, and one of her boobs. Later the robotic parts on her boob is gone.
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The animators made Goroh's shirt image MUCH more simplistic than in the games.
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Baba does not work for Zoda in the game series. He and Bio Rex are "neutral" characters. Octoman does not work for Zoda either and is somewhat a hero character in the game series.
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In the F-Zero games, the year is 2650. The writers of the show messed this up. (Reply: The games, according to the F-Zero GX official website, take place in 2560.)