I really wouldn't worry about it. I think all MBPs have at least small issues with not closing entirely flush. Just use your computer and take it place to place and you'll either stop notching it, or it'll actually flatten out.
I used to be concerned with my system when I first bought it last July since it seemed misaligned, but after I've used it pretty heavily, I don't even notice that issue anymore. It doesn't affect function in any way, so just use your system and it'll go away.
The reason why a lot of people are posting sarcastically is because in the past a lot of unreasonable people have complained about lid misalignment; I think this one guy asked for 4 replacements or something because of something tiny like that.
Anyway, don't worry about minor things like that. Just use your computer!