If you're working on a MBPro Retina or Thunderbolt Display, or any display that uses in-plane switching (IPS) technology, your issue is likely image persistence.
I was experiencing the same problem on my Mac with all programs. I would close or hide a window (or Emacs frame), and I could see a very faint remnant of that window (frame). It also occurred when I switched OS X 'spaces.'
After putting it off for some time your question prompted me to finally investigate the issue. I would recommend Apple's article on Avoiding image persistence on Apple displays. The punchline:
To clear the persistent image, allow the screen saver to run for approximately as long as the image was being displayed.