They do not stand for anything
They are simply markings that can be used to sort Pokémon in their boxes, and do not have any special meaning:
If you are sure you didn't mark it with a star, then it could be that your Metagross was traded to you. When traded, Pokémon keep their marks, so this may explain why the star is filled, you may have not noticed the marking at first. If this is not the case, I don't know, they are not meant to fill automatically, so it is either a glitch or you are mistaken with something.