This didn't happen in Colosseum because you had to go to a PC to save. But in XD, if you're going through Mt. Battle, reach the end of an area after battling the area leader, and decide to save & quit, don't do it at the rest house. If you do, when you next turn on your game, the guy won't let you continue, saying that you can only continue if you've cleared all preceding areas. Thing is, I've already done that. I still have my PokeCoupons, and going back to talk to the area leader will just result in the person saying whatever they did at the end of my last battle. So the only thing I could do is have that Abra teleport me back to the main counter, and despite having the correct number of Pokecoupons, the game thinks I can only start from areas 1-3, when I should be able to start from area 4.
So, if you save in the middle of a Mt. Battle challenge after beating an area, teleport back to the registration counter first, otherwise you'll be forced to complete the last area again.
So, if you save in the middle of a Mt. Battle challenge after beating an area, teleport back to the registration counter first, otherwise you'll be forced to complete the last area again.