do you think that it could be my brakes?...it only does it when i apply them.
Doubtful. Most likely pad material was transferred onto the rotor surface when they were at a high temperature. It's very common to see this as people often leave pressure on the rotor after a hot stop. The pad will leave a little streak or footprint on the rotor surface. Trust me, rotors can warp, but don't on the street. You gotta get 'em glowing and by then your brake fluid is useless anyway.you can warp street rotors, i've done it. but it depends on when you feel the vibration. is it only on braking? is it at constant speeds? accell??