Ditto messing with my prestiging

The player prestiging used a Vaporeon to prestige. Probably not a good choice in to Ditto - even though he retains his HP stat and Vaporeon has much higher HP you're still making it in to a strong pokemon.

I typically throw a weak pokemon first (Magikarp is suggested but I can't be bothered to go that far so I often use a Charmander or Caterpie) then swap out to what I actually want to use - cream the first pokemon then move on with the gym.

Also, Ditto is garbage on defence for the same reason. He's just annoying to prestige against - which means you're hindering your own team by putting him in a gym. Then he's going to sit on the bottom so you're not keeping a good spot for yourself anyways.

Their use is likely to come with breeding. For battling, they're useless.