The bug is caused when players attempt to save their game outside a building in Lumiose City, Nintendo says. The company has also produced a map showing the affected area.
Users who claim to have been affected by the bug report that their save files are made completely inaccessible. Nintendo's fix, when released, should be able to restore the saves of players, the company adds.
Both physical and digital versions of the game are said to be affected.
Pokemon X and Pokemon Y launched worldwide last week, selling over four million copies in its first weekend on sale.