It could be that you have got a cracked or glitched Pokemon or perhaps you might have hacked your cartridge or your save file got corrupted for some reason.
here is a link for the known glitches in X and Y: http://bulbapedia.bulbagarden.net/wiki/List_of_glitches_in_Generation_VI
on the link among the known glitches there is a "save corruption glitch"
"It has been reported that some save files of digitally downloaded copies of the games have become corrupted. This issue has affected other games downloadable on the Nintendo eShop such as Mario Kart 7 and Mario & Luigi: Dream Team."