I send it out for battle but then the sprite disappears! When I use a move it is still invisible, what is wrong?
According to Bulbapedia:
tl;dr What you are experiencing isn't an official glitch.
In my opinion, though, it may be the cartridge itself. Old cartridges are known to bug out at times, and the older they are, the greater these effects become, such as with your Gengar in your situation.
Hope I helped!