Did you did anything crazy related to Team Rocket like creating an all Team Rocket team or simply name after your character to somebody in Team Rocket?
I have never created a team with Jessie and James' Pokemon, but I named some of my party members with their names. I have an Arcanine named Kojiro and a Dustox named Musashi, a Ninetales named Jessie and a Scizor named James... I also have a Garchomp named Giovanni...
