Remember how when Harry was sitting on the sorting hat, how he still got sorted into Gryffindor, although he also held the qualities of a Slythein? Remember how because he really want to not go into Slytherin he wasn't placed in Slytherin. Well, that is what happened.

I'm thinking that maybe Hermione was place in Gryffindor because she wanted to be placed there. Even though she held the qualities of a Ravenclaw.

Dumbledore also said that it is not your qualities, but you choices that get you placed in the house you are placed in. So, that is what I think happened to Hermione.