Vanish/Doom was never meant to work though. It's correct the way it is in the GBA version, where it doesn't work.

It's nice that RPGOne and SkyRender fixed those bugs. I don't really see how that has much to do with the GBA version though. They can't just reuse something a fan made and put it on a GBA cart.

The only new bug I know of is one that makes Interceptor protect others than Shadow, but I never encountered that bug myself. Another minor issue is that the game sometimes slows down when there's a lot of action on screen, due to the CPU of the GBA being weaker than that of the SNES.