When I'm building, once I get to sanding stage, I have foam cut out to sit the cuitar on, stops it from getting scratched and dinted up.
As others have said, it's simply that you've skimmed over your sanding process rather than going into fine detail.
As far as sealing - I use a cheap 2k clear (if its a transparent guitar) spray several coats, wait a week, sand it back and repeat till all the grain is sealed.
Another thing, if you're getting these kinds of scratches in your wood, you probably want to read up on your paint process as you'll get them in your clear too.
Good luck!