Ok here's my situation Ive been in Europe for about 6 months now and I am leaving back to America in a few months I entered through Germany but I'm leaving through Spain and I know that my US visa was supposed to be only 3 months, however I am also a Spanish citizen but my paperwork came through about three months ago and to get my EU passport I have to do it in the Spanish embassy where I'm registered in Miami, but I have a Spanish birth certificate here with me, would they give me any trouble? I'm coming back next year and I don't want to get blacklisted
As long as you can prove you have Spanish citizenship you should be fine.
Do you have any paperwork stating that you have to pick up the passport in Miami? That should be sufficient proof of your Spanish citizenship.
You should not have any problems because:
1) As a Spanish citizen you cannot be banned from entering the EU.
2) You are leaving from Spain, not from Germany - it is the Germans who ban people from entering. I don't know the punishment for overstaying in Spain, but that point is moot because you are a Spanish citizen and thus did not break any rules.