I had an issue with my 2012 MBPR 15" screen calibration. I cannot offer a definite solution, because it has come good and I am not sure why.
I noticed that photos seemed to require highlight and shadow correction more than seemed usual. I looked at this colour checker:
The 3 whitest squares were almost indistinguishable, as were the 3 blacks. The 5th row from the top was almost white.
I used a Spyder 4 Pro to calibrate the screen (or is profile the correct term?). That reduced the contrast but still the 2 blackest and 2 whitest squares were blocked. Also, skin tones all looked like there was a layer of pink makeup on them. The advanced analysis showed that I was getting 100% of RGB, but with a very s-shaped tone curve.
I also had a go at using the Apple calibrator. It actually did an OK job but with similar issues to the Spyder's.
I changed the profile a few times, using various screen and printer profiles that show up in the Colour tab of the Display section in System Preferences. (They have accumulated over time and changes of equipment).
I tried screen-sharing with my old white 24" iMac: despite its age it was showing better highlight and shadow detail (and I do prefer its matte screen).
I also plugged the MBPR into my cheap LCD TV via HDMI. I created a profile for the TV using the Apple calibration tool again, and photos looked OK.
Now here is where it got interesting. Some time after doing these various bits of playing around I noticed that the MBPR was showing the above checker satisfactorily on its own screen. I the re-did the Spyder 4 process and the resulting calibration is really quite good. I also looked at a white and a black colour checker, and shade 5 is distinguishable form 0, and 254 from 255, and no "pink makeup" effect.
I notice that others have had issues with screen calibrators on the MBPR, both Spyders and Xrites e.g.
https://discussions.apple.com/thread/4063915
http://www.trustedreviews.com/15-inch-macbook-pro-with-retina-display-2013_Lapto p_review
However, others have reported good results:
http://cdtobie.wordpress.com/2012/06/19/retina-display-macbook-pro-for-calibrati on-and-photography/
So something I did made the MBPR stop its high-contrast behaviour, and the Spyder then was able to do a good job. I wish I had noticed precisely when it came good.