it was also confirmed that wonder trade was not to blame for the problems. i've wonder traded... 50+ times now? no bad egg for me.
it looks like the true culprit was the person's system or sd card being faulty.
and it's not the fault of hackers either, before anyone brings that hysteria here. this was reported day one and hackers are still looking into all the secrets of the pkx format, and are also looking into how to inject the mons back into the game (that means they can't do that yet, ergo it is impossible for this problem to be related to hacking at all).
so wonder trade in peace; there's a very minimal risk of that happening to you. if it hasn't happened to you yet, it probably won't.