Eureka! I found what was causing the glitch. Instead of lowering the HP IVs to automatically set all IVs to 31, I should manually input all IVs. This has stopped the Ability Glitch in Gen-3.
One Request: Can you Add a Feature to Change Forms of some Pokemons. Like; landorus, deoxys!
I'm Just loving how this project is going. Much Appreciations.