It really depends how bad it is, a picture would help assess it. Mine wasn't "perfect" either, when the lid was covered the corners had noticable flares. That I just dealt with. But if yours had noticable gaps between the top panel and the body, I suggest you lossen the side screws, press down on the top panel and re-tighten. That helped me eliminate most of those and i'm quite happy with it.
Because the casing Apple used is quite thin and flexible, it can make fitment a nightmare if you're a perfectionist. Plastic traditional casings have those issues too, but typically not as bad.