Got the same problem. I have my N9 for 2 weeks now; I did not particulary protect the surface, but I always avoided to pack it with keys or similar sharp objects. And there it is - a tiny little nasty and annoying surface scratch. I have expected more from the Gorilla glass. And if it really is only the surface coating - well its still annoying.
There is not much to do to protect a touchscreen - it still wants to be touched...
I really am a little disappointed