"Legit" means caught/bred in game without hacks, doesn't it? (And I suppose event Pokémon also count in that as they're given away by Game Freak themselves.) I don't remember the exact species of it, I'd have to ask her again, but she stressed that it was definitely legitimate.
Said girlfriend that I mentioned also got a shiny Shaymin that was definitely not legit through with no problems, so yeah, there's something wrong with the checker. (And yeah, this one I'm not just going off of plain word by. She showed me it. If you really need more definitive proof, I can ask her to show me it over trade again and I can take a picture of it. She's asleep right now but that shouldn't be too difficult once she wakes up.)
EDIT: So, this is what happens when you try to make it out as if I don't know what I'm talking about - I go to find sources. Yes, while I can't find what my girlfriend's friend's claim as proof, I've found much more incriminating stuff.
Here's the hacked Shaymin I was talking about:
This was given to me by her just so I could prove a point (I asked her if I could borrow it).
And now, I'm going to link you to a bunch of Tumblr posts of people complaining about legits not getting through, ending with the most definitive (warning; some have vulgar language): 1, 2, 3, 3, and 4
And if you search online there are a lot of people having the exact same problem, so it's not just me pulling something out of my butt.