So apparently, wonder trading is dangerous now. Wonder trading could cause mystery eggs to appear, no not bad eggs, they're literally called Mystery Eggs. So far bulbapedia says this about it:?
"Occasionally, a player will find an Egg that randomly appears in one of their PC boxes with its data set as being obtained from the Mystery Zone at 0/0/2000.
These eggs are speculated to be caused by checksum errors when trading Pokemon via Wonder Trade, and unlike the Bad Egg of previous generations the Mystery Zone egg can be harmful to Pokemon in the same PC box."
Do not use the wonder trade mechanic anymore until Game Freak creates an update to fix this glitch, if you happen to find mysterious eggs in your PC, do not lay a finger on it, or try to do something crazy, like hatch it. Instead move all your pokemon out of that box into another one with the eggs.?
XHero111 : Credit to him for telling me about it.

Nice to know. Now when I get a 3DS with Pokemon X, I know something to avoid!

It's unlikely I'll be getting a 3DS, though. But a kid can dream, right?

hilacle : Awww, You beat me to this thread. Anyway. I don't think we need be to concerned about the Mystery Egg. It usually only happens when your game suddenly disconnects from the internet. But, I'm still not wonder trading. Better to be safe than sorry.

An interesting theory from a friend of mines,
Mdragon1 :
In Pokemon G/S, the egg received from Mr. Pokemon is called the mystery egg.
G/S was created in the year 2000.
The mystery egg states that it was obtained on the year 2000.
Coincidence? Or not?
It could be that a Kalos trainer gave the egg to a Kimono girl.
The kimono girl gave it to Mr. Pokemon.
Mr. Pokemon gave it to Gold/Crystal
Gold/Crystal gave it to Elm.
Elm gave it to his aid.
His aid gave it to you.
The egg also states its from the mystery zone. The mystery zone, is a real place, infact, a glitch place.
More info on the mystery zone here:?http://bulbapedia.bulbagarden.net/wiki/Mystery_Zone

More info we've aquired:
1. They're caused by bad coding, obtained randomly by using wonder trade.
2. They make Pokemon disappear by cloning themselves.
3. The eggs are from the mystery zone, a glitch location in Diamond, Pearl, and Platinum.
4. The eggs could disappear over time, and a Pokemon may come back. But this is however rare.
5. The hatching ratio increases with each step.
6. When used in battle, the egg may be level seventy, and it will struggle.

hilacle : I wanna hatch one!

If you have a Mystery Egg, here are some of the things you should / shouldn’t do:

1. Do NOT touch the Mystery Egg! That means no checking moves, stats, anything. It may have an item attached, do not attempt to retrieve the item!

2. The box the Mystery Egg is in is immediately QUARANTINED. Immediately remove ALL Pokemon from the quarantined box. PUT THEM IN THEIR OWN BOX AND WATCH THEM CAREFULLY. Once the Egg has been in a box, that box will be PERMANENTLY infectious.

3. Do not, I repeat, DO NOT attempt to withdraw the Mystery Egg. Do NOT attempt to hatch the egg either.

4. Your primary goal is to save all your Pokemon from infection. Treat a Mystery Egg like you would a zombie pathogen that spreads via air. Keep it as far away from EVERYTHING as you can.

hilacle : Actually the mystery zone exists in all Pokémon games, 4th Gen and onwards, so it's not exclusive to DPPt. The mystery zone is just famous for its existence in DPPt because it was easier to get into it in those games and it was used to get to event legends. I should point out that mystery zones are spaces in between the different areas. For example in Sinnoh. Usually the areas past trees or water that you can't reach are part of the mystery zones.

I'm going to sticky this for now, because it sounds pretty bad. Once it get patched, I'll close it. Hope not too many people have to experience it. I wonder if maybe Gamefreak was pressed for time towards the end. This is two game breaking glitches.
 
~Stickied~

This is terrible!! I wonder traded 100 times this week and I never even bothered to check my PC.

XHero111 : When you said "Awww, You beat me to this thread. Anyway. I don't think we need be to concerned about the Mystery Egg. It usually only happens when your game suddenly disconnects from the internet. But, I'm still not wonder trading. Better to be safe than sorry", my Internet has a habit of disconnecting like 10 times per day.
 I don't have a 3DS of my own, and not Pokémon X or Pokémon Y, but if I get one I can say hello to the Mystery Egg. My internet is so bad that once I actually lost connection during a battle on the internet with someone. I asked for a rematch, but he was annoyed because my internet went off when it looked like I was losing badly.

Thanks for saying this, and I'll be careful in the future.

                   Thanks for the note ~
                                                               ~Pikachi~

Well this sucks now! I can't continue with my wonderlocke, well I'll have to wait for just use the pokemon from the box I already have...  

I've done some testing. I traded all my pokemon to a friend, restarted Pokemon X, and then after I caught 5 pokemon, I wonder traded all of them (and got decent pokemon), I'm still doing it, (well, except with the pokemon on my team (Like my Protean Greninja), and still no Mystery Egg, I doubt most people will get a mystery egg, but still, You should still be cautious of the danger... OF THE MYSTERY EGG!

You could still wonder trade, just make sure your internet doesn't disconnect a lot, and be safe. Also if you do get a mystery egg, just don't touch it and remove all your pokemon from that box. GL not getting a mystery egg, guys.

One thing that Im GOING to clear up : Mystery eggs can actually appear ANY TIME. You don't even need to wonder trade. They can also appear if  you get a pokemon from a trade or wonder trade that has edited stats.

hilacle : I am addicted to wonder trade, but I don't know much about this. What is the probability of it getting there? I don't want it, but I don't plan on giving up wonder trading...

I did a wonder trade once and I thought it was pretty weird, I put a pokemon out there but I never got anything back. Oh well, at least it was something dumb like a bunnelby. I wasn't really expecting anything in return, so it isn't a big deal or anything. I just use the GTS trade and trade with friends or trade pokemon I want with other people. I want to get an armaldo, an articuno, an omastar, and a kabutops. Those are all good pokemon in my opinion and I will trade a pokemon in return for them Just not through wonder trade XD, I will probably get nothing back again. 

I owned Pokemon Y for a month and a half. I will never play the game after hearing about this. I hope my Chesnaught's fine.

Ohhh man, I totally love Wonder Trading. Stupid Mystery Eggs!

I feel like I've been a real joykill to you guys so I want to clear up a few things.
SadSecrets :
zelda2 :
zanderlex :
~Pikachi~ :
GreenTurtle :
Hidden Phantom :
Razor-987 :
SuperMariofan908 :
Mistress :
Bulbapedia has deleted the mystery egg info, I can't seem to find it anymore on the site anymore, so they must have thought the mystery egg rumor to be false. PLUS, I've gathered no info on mystery eggs appearing ANYTIME.
98Gamingstar : Where did you find this info? Provide a link if possible, or any source of proof.
It has been a bit past a month and Game Freak has not make an update fixing this problem when it took them a couple of weeks to create an update fixing the Luminose City Saving Glitch, so maybe this is just all fake? That we've been deceived?

I want to say Sorry for being a buzzkill, so continue wonder trading ^^

Local Mods :
I'd like this thread to be close.

hilacle : Mystery eggs are still going around (I know because I got one yesterday..) And BTW Its just rumors that mystery eggs can just appear out of nowhere plus this guy on youtube had never done a single trade, never really had his Wi-fi on and he still found one.