Sounds like you are sanding through the clear. The best way to stop this is apply 2 or more coats of clear before a light sanding. If you are spraying this will be easy, brushing not so easy.
Use a very fine sanding block, 220 or finer, and very lightly sand. After sanding wipe the door with a tack rag to remove any dust. The thicker the clear coat the less likely you will sand though it.