Pokemon XD Controller Bug with Native Controls Off

[Danphibia]

I am soft resetting for shiny Pokemon in Pokemon XD Gale Of Darkness on Wii U. However, after a random amount of soft resets my controller will stop working or the game will freeze on a black screen after resetting. I found out that this was because native controls were off which can’t be turned on for Wii U. I would like to know if this is something that can be fixed for native controls off or if it is just an issue specific to Pokemon XD.