Why does my Greninja get boosted EXP?

Your Pokemon may have the ability Anticipation

Anticipation causes the Pokemon to shudder when you're in battle with an opponent who has a super effective move or a one hit KO move. Depending on what the rules for it are in Gen 6, it may also trigger when a Pokemon has Self Destruct or Explosion (this varies between previous versions)

It will not notify the Pokemon in the case of a super-effective Hidden Power, Judgment, Weather Ball, or Natural Gift, as they are normally Normal-type. Counter, Metal Burst, and Mirror Coat are also not detected.

Boosted EXP without being traded may be a result of the EXP Point O-Power, which somebody might have buffed you with. If you were connected to the Internet through the Player Search System (PSS), this is the most likely case. To get this O-Power yourself, you must talk to Mr. Bonding in the Anistar Pokemon Center.

Also, it seems that increasing your Pokemon's affection and related stats through Pokemon-Amie has a chance to increase EXP gained along with a host of other effects.

There is an additional way to get boosted EXP that has yet to be mentioned (though it obviously doesn't apply to your situation here).

Aside from trade (which you already mentioned), Pokemon will get boosted EXP if you stop a level-based evolution from evolving.

My Weedle, Steve, is now level 8 and gets boosted EXP for every battle we're in. Were I to let him evolve into Kakuna (this naturally happens at 7), this boost would stop.

My Pikachu gained a similar boost in Exp gains. I noticed she had a strange purple dot on her head in the Pokemon-Amie tab, and went to play with her to see what it was. The dot was gone, but she looked a little sick at first, but that went away when I fed, pet, and played with her.

When I sent her out into battle, she swayed side to side, and the game said, "Harley [my pikachu] looks a little out of it." and from that point on, she's been gaining bonus Exp.

My Absol has been gaining a boost as well, but I haven't been on Pokemon-Amie with her at all recently. But I did get all the medals on Super Training with her. So I'm thinking that's why she's been getting a boost in experience points after winning battles or catching Pokemon. So that could also be why Greninja is gaining boosted experience points. :)

Okay so I caught a Gible in the wastelands, and I've never battled with it (not even had it in my party) until today, and in my first battle, it gained boosted exp. I've never super trained with it, nor have I played with it on Pokemon-Amie. I have no idea what is going on with it. But it would seem that other Pokemon do get boosted exp when played with and their affection goes up.

In all honesty, this could be a glitch from the game itself. Infecting random Pokemon. Because none of my other Pokemon are exhibiting this symptom. I'm thinking about contacting Game Freak or something b/c I don't want my progress erased. You never really know..

Also, I've done PA (Amie) up to two hearts, and that Pokemon never gained boosted exp. I'm gonna try and do more research on this.

Yea I believe that maxing out a pokemons evs causes an exp boost. I was teambuilding and I noticed that after I ev trained my freshly bred team, the exp boost happened. Amie also causes this with a certain amount of affection, but pokerus does not affect it, as that doubles ev gain and not exp gain.