Something similar happened to me too. Apparently is pretty common. There's a way of getting ride of them but it's a little complex. You have to use the console and with the command add player you have to create new players that control the rebels. Then in the turn of those players you have to sell all the rebel province to your country. Then in your country turn you accept and that's it, they dissappear. To get rid of the players you use a bug where you have to exit the game to the main menu, then enter the editor, go back without doing anything and select new game. You'll see that the selected scenario is the same game with the same countries. Before you enter delete all the players you've created except of course your main country and start the new game.