It happened to mine and it has happened to many, many other people, with numerous reports here on GAF. It hasn't happened to everyone though.
Yeah but you make it sound like its happened to a lot of people, which proportionally it more than likely has not. There's a reason why it's called the vocal minority/silent majority.
I'm not knocking your experience and understand if it comes off that way I just can't help but feel it's not really that big of an issue after being a big proponent of it but then never having any problems past wipeable smudge lines. I figured if anyone should get screen scratches it would be me since I carry my 3DS around in my back pocket most of the time where there's a lot less room.
I do fully agree that the system design is poor due to the fact that the two parts can make contact while closed though. I just don't feel that this is the "RRoD" that many people want to make it be (sorry if that's a poor analogy) yet I still constantly see people bringing it up in new threads "but I don't want to pick one up yet if screen scratching is still an issue".
Edit: And just to be clear I've seen the pictures people have posted, I understand that it has and does happen, I just don't believe it's as wide spread an issue is all.
This is getting a bit off topic though, as for MGS3D I'll save my judgements until I can see the game in person. The 3DS itself definitely looks interesting though, not sure if I like it or hate it.