So, is that bad egg thing still out there?
From what I've seen from lurking the pokemon reddit, Smogon, and Serebii;
All but one of the posts relating to the 'bad egg' point to each other and ultimately to a YouTube video which was dated the day after X/Ys release.
The only other post is unconfirmed as to its origins (ie. although it's suspected to be from wonder trading - the egg states 'recieved via Link Trade', it hasn't caused the user's 3ds to explode, all their pokemon to turn into Farfetch'd, or any other horror stories).
The Wondertrade subreddit has no mention of users receiving 'bad eggs' and the entire subreddit is - as hinted by the title - devoted to WTing pokes.
So... at the moment there's no apparent reason for hysteria over it. It may be caused by a communication error, or invisible solar death rays, or hackers, or... who knows. But as it's not reproducible, and in who-knows-how many million WTs there's only been one or maybe two reported instances of this... it's hard to say.
The only thing that the game devs could do, if it's not a solvable issue (ie. no known way to reproduce), is give us a way to dispose of eggs. That way if we do - somehow - get a mystery egg, all that needs to happen is we just make an omelette. Erm, I mean, dispose of it humanely.
tl;dr version - it hasn't been reproduced and there's no official word on the website - a game-wrecking issue for one of the biggest franchises would be dealt with quite quickly, I'd think. (see: Lumiose city save glitch - announced with cause and patched fairly quickly)