PokéBase - Pokémon Q&A
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Just a straight-up curious question. At some point I think that it was probably because of sprite miscoloring, but any other ideas?

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They originated from Game Freak logic.
But seriously I think it has something to do with how they wanted to take better advantage of the GBC's new color features.
I know this is a bit old now but I'm fairly certain it was originally a glitch. Certain IV values in gold and silver would inadvertently change the hex number for colour by one value, which is why most shinys are almost random in change. The term shiny was first officially used in Pokémon black and white. From gen 6 onwards, a shiny colour was manually determined rather than shifting hex values.
Why would they have a shiny locked red Gyarados if it's a glitch?
Because they liked the glitch and decided to use it? This kind of thing happens in game development, where an accident occurs that actually enhances don't aspect. It's not uncommon.

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Shinies originated in Pokemon Gold and Silver for the Game Boy Color. Unlike Red, Blue, and Yellow on the Game Boy, which was just black and white, Gold and Silver actually had color. Game Freak likely wanted to take advantage of the GBC's color features which were not available on the original Game Boy. The term 'shiny Pokemon' originated from most of the fanbase, but Shiny was officially used in Pokemon games for the first time in Pokemon Black and White.

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