The latest Pokémon X and Y games bring many new mechanics to the games, including many new online connectivity features. One of these features is called Wonder Trade, and it allows players to anonymously trade Pokémon with someone else online without knowing what they will get in return whatsoever. It’s a neat enough feature, but a malicious virus-like hack seems to have entered the dataspace of the Wonder Trade.
Some people have reported receiving a Pokémon that is labeled as “Bad Egg”. When it is transferred to the Box, it multiplies until it completely fills every space and subsequently overwrites every other Pokémon inside as well, effectively deleting all your hard work. The “Bad Egg” hacked Pokémon cannot be released or traded to someone else, thus breaking the game. It is currently unknown what happens if it is traded directly into your party, but it probably does the same thing.
Regardless, until Nintendo or GameFreak arrives with some sort of solution, it is recommended that players stay away from the Wonder Trade feature, just in case. Everything else seems to be in working order however, so other than that, feel free to continue enjoying Pokémon X and Y. We will be sure to let you know as soon as this is resolved.
UPDATE: The post from Bulbagarden that reported claims of the rumor has since disappeared. Neither Nintendo nor GameFreak have confirmed this as an actual glitch/hack, so just be wary of Wonder Trades for now, just in case.