I would reckon that it's because the bag will have spots & the 3D doesn't.
Because the bag target has a spot for you to aim at, you aim at that spot. A 3D doesn't have a distinct point for you to concentrate on & therefore you end up shooting at the entire target, not at a particular point. Take a magic marker & put a spot on your 3D, where you want to group your arrows & I would guarentee that your grouping will improve, instantly. Shooting instinctively requires a lot of focus & it does help to have something to focus on