Pokémon Omega Ruby and Alpha Sapphire's creepiest moment happens so fast, most players probably miss it.
You've likely heard about Pokémon X & Y's "ghost girl," that unsettling incident that happens with a weirdly-animated Hex Maniac character. This is different.
When you tackle the Elite Four, Pokémon's version of final bosses, one of the trainers you fight is named Phoebe. Like every member of the Elite Four, Phoebe has a schtick: she uses ghost Pokémon. Her section of the game is ghost-themed, too. Before you walk into her room, you see this:
It's a neat effect, but nothing particularly spooky. Then, when you talk to Phoebe, she tells you that she trained at Mt. Pyre, which you might recall is the location where the people of Hoenn bury their dead Pokémon. In fact, according to Pokemon lore, the lady at Mt. Pyre that hands you the orb you need to awaken Kyogre or Groudon is Phoebe's grandma. Basically, everything about Phoebe—from her background, to her Pokémon selection, is kind of spiritual. Anyone that challenges her can see this.
What most players might miss, however, is something that happens in the corner of the room right before you battle Phoebe. There, you'll find a chair. The Elite Four member before Phoebe, Sidney, also has a chair in the room—presumably so he can sit there while waiting for trainers to challenge him. It's the sort of small, innocuous detail that you don't pay attention to, because it's literally in the background.
But Sidney's chair is right next to him. Phoebe's, for whatever reason, is all the way behind her. That's because she's not using it to sit in it herself. Instead, a ghost girl is happily sitting down on the chair—you'll miss this detail unless you're looking at the chair during your conversation with Phoebe, since this ghost girl only flashes on the screen for a split second. We've freezed the frame here so you can see it:
But when it happens live, like it does in this video by Pyropuncher around the 1:25 mark, you might not even notice:
It doesn't help that the ghost girl isn't always particularly visible every time you 'encounter' her. In this footage by giancarloparimango11, you do see something, but it looks like a way less distinct white blur.
Personally I didn't notice the ghost girl at all during my playthrough, and she doesn't appear when you re-challenge Phoebe after becoming the champion, either.
Either way, you'll note that after the ghost girl flashes, the screen turns black, and then the camera angle changes. The camera then seems to stand up from the chair, and walks slowly toward the player. Without knowing that there is a ghost girl back there, the fact the camera angle changes might seem vaguely funky, not sort of ominous.
That's not the only time this character appears. After the point-of-view change, the camera fades to black once more, and then the camera angle changes yet again. This time, the ghost girl appears to be right next to the player:
See that face right next to the player's neck, on the left? It's tiny, but it's definitely there. You can make out an eye and an eyebrow and an ear. The ghost presumably walked there during the funky camera angle time.
When the battle is over, you talk to Phoebe from the same angle, but the ghost girl seems to be gone:
Still, though. It's weird, right? What gives? Who is this girl?
Phoebe does mention that she has the ability to "commune" with ghost type Pokémon—but what you see in the corner isn't a Pokémon. It's a girl. Pokémon have been known to be able to cast illusions that make themselves appear as humans—Zoroark can do it, for example. Maybe that's it. It seems unlikely, though, since Zoroark isn't a ghost Pokémon. It's a dark-type Pokemon. Phoebe doesn't use those!
Another theory I've seen floating around is that maybe that ghost girl is one of Phoebe's dead relatives—I've seen at least few errant comments that claim that it's actually Phoebe's sister, who dies in the manga version of Pokémon. But I can't actually find mention of this on sites like Bulbapedia or the Pokemon Adventures Wiki. I've also seen more morbid theories, like the idea that maybe this girl is Phoebe's dead daughter. But again, there's nothing actually in the game or in the lore that supports this idea.
I will note that the number of paranormal/ghost-related easter eggs seems to be increasing. Makes you wonder if Game Freak is slyly trying to set something up in the future, perhaps somehow involving the currently-unreleased Hoopa. But who knows! Remember, the first thing Phoebe does when you meet her is give you a big, hearty laugh. Maybe this ghost girl thing is just Game Freak pulling our legs, having a little bit of fun.