Quote Originally Posted by Hsu
Sounds like just a random glitch. I remember stuff happening like that in the old Red and Blue versions with Missingno, though I'd imagine they had fixed that bug by now.
I did encounter a missingno in the game about two weeks ago and I ran away from it. It looked like a big question mark in a ball, like the empty spaces in the pokedex. Do you think that had anything to do with Latias dissapearing?