So yeah I experience the exact same problem on my new RMBP 13'' (screenshots here: https://discussions.apple.com/message/20925037#20925037)
It doesn't really matter what desktop programme you use for reading PDFs, it gets distorted everywhere. I mostly read on Preview, but tried others as well, and they produce the same issue (except when reading PDF in Safari, or Chrome, then its fine).
Do you think if it's an arithmetic problem it can be fixed by a software update? Or is it something we'll have to get used to and live with, from now on?
I didn't have time to visit the Apple Store so far to ask them, but I'll definitely do so.
Maybe it's just a problem with our particular Macs, and not with all RMBPs?
If you are seeing it in other places — I do too, but mostly in Preview — then it is a problem with the toolkit. It's certainly just bad programming. Does Apple care enough to fix it? That's a tough one. It's been a problem for a while and no fixes. Like the Thunderbolt USB audio problem: they no about it, but no effort to fix it.
A bit off topic, but I also experience the choppy scrolling issue on Facebook, and also whenever the website tends to be a bit more complex. They haven't come up with a fix for this either. :S
But what makes me truly disappointed is the PDF issue, since my main motive for replacing my old MBP with a new Retina was the sharp text that is much more convenient to read when it comes to working with lengthy PDFs (my old one kind of hurt my eyes since it looked very blurry compared to paper text, and I just couldn't stand it, i'm quite picky when it comes to my eyes ).
Anyways, c'mon Apple, this is just too many bugs for a single product! They really must do something on these if they want to keep their customers....