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The Hack doesn't have any major edits done to Hex code or whatever, just some edits of different trainers, some Pokémon Sprites and Stats and some encounter areas. No idea what caused it.
Game worked fine before I edited the sprites, but it was really just the Pokémon sprites, and they all look...
So, I imported some sprites to my Fire Red hack, namely a new sprite for Ninetales, I imported the palette, and the normal front and back sprite look perfect, but the shiny versions look all messed up.