Yeah, over on the MacNN forums there is a thread about the slot CD drive etching grooves on CDs, which was met with some skepticism and some agreement. I was on the skeptical side until I examined a CD that had been in the drive when I had moved my Macbook from one room to another. It had a number of very faint, but definitely present grooves in it that looked like a vinyl LP record. Eeek! It could still read the CD (and it was a CD I burned and thus could reburn) but still this apparently is a bit of a problem.
Some have taken their Macbooks back to Apple for repair/replacement under Applecare but their CD drives still grooved up their CDs. The jury is out as to whether this is something that needs to be fixed by Apple, or it's just a result of the drive being extraordinarily thin and sensitive to tilting. Personally I'm in the 'this is the physics of spinning objects within something of tight tolerances' faction. CDs spin at some pretty high RPM when in use, and if you tilt it, gyroscopic forces being what they are will probably make it so something in the drive that shouldn't contact the media while it's spinning is going to if you move the machine around.
Check your CD to see if there are any grooves etched into it. You could take it back to Apple to see if there is a repair possibility, but I am just going to make sure that I don't move my Macbook while there's a CD/DVD in there spinning.