I bought my iPhone 2 weeks ago this coming Monday and after a week, I found a tiny scratch on the screen. It's about half an inch long, shallow and it's at the bottom part of the screen frame and just touches the screen a slight bit. You can't feel it with your finger or finger nail. It's really hard to see, like it's not actually the glass that's scratched (just the oleophobic coating, I suspect), but it's still annoying and it bothers me because I know it's there.
I haven't dropped it, or scratched it. I keep it in my pocket when I'm out on it's own (no keys or coins or anything else) and when I found the scratch, I was using the iSkin Solo FX case.
I was really disappointed when I found the scratch coz it's my first iPhone and I love it to bits. I didn't put a screen protector on it because my iPod touch that I've had for 2 years now never had a screen protector on it and the screen is still perfect. The iPod touch itself has a few scuffs on it from when I dropped it as I was climbing out of my car but the screen is perfect. Anyway, due to my past experience with the scratch resistant screen I didn't think I'd need a screen protector.
Let us know what they say about the scratch at the Apple Store ASAP. =) I'm hoping they replace yours so I can use it as a precedent when making my claim.
Good luck at the genius bar. Hope to hear some good news from you soon.