I feel ya. The same happened for my Black 2.
Anyway, it just means the file that was saved most recently has corrupted. If you play legitimately, it is most likely that the game encountered some sort of error whilst saving, and there isn't much you do about it. It is a rare thing, and shouldn't happen again.
Since the game keeps the data from the second last time you saved as backup, it will continue the game from that moment.
The easiest way around this is to simply save the game twice before turning off. I know I've done this since I got the save file error, it left me pretty data-corruption conscious.