The Japanese Pokemon Global Link has put out an update regarding stricter hack checks that are to come to the game. If you have been caught with a modified save file or modified Pokemon, then you will be unable to participate in Rating Battles or in Battle Competitions. If you are caught having done this multiple times, you are to be hit with stronger consequences beyond blocking from Rating Battles, which have not been detailed, without any warning. Those who have already been confirmed to have done this will have consequences enacted soon. This follows recent instances of save data loss for innocent players after they have encounter certain people with modified data. We'll keep you apprised of further developments
Pokemon X & Y