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I guess it's a bug... Try to bang your game to the wall and may it will work, just kidding.... But seriously, i don't really exactly know how to fix your problem but i'll try my best to see the solutions for your problem...
I'm so attached with my Crystal, even though I've restarted my game again and again, I'll never depart my Crystal, that goes for my Emerald and my Yellow too...I don't why but they are my favorites...
In my own suggestion,Yellow came out months before the anime was released and it was based on the anime and th red/blue versions...Have you saw or read the pokemon comics? Red and blue was based on the comics...
Totodile is "D" best of all,for me...I like, I mean I love water type pokemon and I surely love totodile especially it's 3rd form,Feraligatr....................xD