I only have the paths in the one group which is inside the other group. I only work with SMD parts (with the exception of headers and wires and Nixie tubes) and have made hundreds of parts for myself and I always have both layers.
How did you do that? I would guess that you edited some through hole part that makes Fritzing think this is supposed to be on both sides at the same time. If I needed and underside part I would just swap the copper1 for copper0 in the svg and make another part. Not a fan of copper pads floating around on the underside of a PCB, plus not many people double load, so I would prefer just copper1.
