You know if you extrude a face -- all the edges inside the face will create a face aswell... what I think is happening is you're creating perpendicular faces inside your extrusions. For example -- take a rectangle made up of 9 faces (3x3, like a tictactoe board) and extrude it up... regardless of if all the faces are combined to a single object. You will not get a box from that extrusion... you will get 9 boxes.