[Script] 2 Pokeballs at Prof Oak's Desk when there is normally one.

Hello. I've changed the starters in my ROM Hack to Snivy, Froakie and Litten. However, when me and my rival get our Pokemon, there are still 2 Pokeballs at the desk. Even after I deliver Prof Oak's package there are 2 Pokeballs and they both say 'This is Professor Oak's Last Pokemon'. Any Help?

Pokeballs are usually Person sprites in the game. To make them disappear you usually need to clear a flag or var that it is attached to. Do you have a flag/var associated with the pokeball? If so, does your scripting clear the flag after you and your rival pick your starters?