Yeah, there is a great chance that Bad Eggs appear in Generation VI.
However, it should be noted that the Bad Egg isn't a mistake. The Bad Egg was put in the game purposely by developers so if someone tried to hack the game, the Bad Egg would appear and say 'Nah-ah, not on mah eggeh watch!'. :3
According to this, you can't trade eggs over Wonder Trade, so that would refer to the Bad Egg. It also states that they have seen only one instance of the Bad Egg through a video, so it's possible that the Bad Egg glitch is fake. This is easily backed up because the 3DS currently remains unhackable (to the internet, anyway. No one has gone viral with it yet.) So yeah, it's just false fear.
However, if you do see a Bad Egg come into your game via Wonder Trade, you're screwed. Sowwy. c:
Hope I helped. :)
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