Hello Kaphotics. Thanks for the feedback. Sorry for the late response, I had cheats disabled in the emulator.
Edit: It seems like according to Bulbapedia, having a Pokemon with a Pokerus of 0 is not legitimate. I guess I may have unknowingly cheated in the game.
Hello, I got a Pokemon Ruby (gen 3) save file (.sa1) that had Pokemon with Pokerus that I got in-game without using PKHeX. But, when I opened my save file with PKHeX, the box for ( Infected) is left unchecked. I think it might be a bug.