Nintendo has confirmed the bug and issued official advice about how to avoid it.
If you become affected by this bug, people have reported fixing the issue by removing the SD card, then resetting the system and starting the game again normally. You will lose any progress between your penultimate save and the glitched save in Lumiose City, but your game should be playable again. There is currently no solution for any digital copies afflicted, but we'll keep you updated.
It has come to our attention that there's a bug in Pokémon X and Y that could render your save game unusable, although I'd like to stress that this has not yet been confirmed by Nintendo.
The bug is simple: saving the game while outside in Lumiose City may render your game unable to be loaded again. To avoid the possibility, exit the city or enter a building before saving.
If Nintendo make an official comment regarding this issue, or release a patch, we will update accordingly.