anti reflective coating issue aka staingate. have been affecting all macbooks with retina display since it was introduced in 2012. there's no solution that i'm aware of unless you
1) not clean the display
2) not to let it come into contact with any kind of object
3) not pack the laptop in a backpack full with other things as pressure will on the chassis will cause the display to come into contact with the keyboard and either dirty the display or scratch the coating
4) keep it away from heat (like using it on clamshell mode)
if your macbook is under apple care they'll replace it for free. if it's past the warranty period likely you'll have to pay ($800 if i'm not wrong, maybe less or more now) unless you have some very good reason to explain. even after replacing the issue will be back after 2 to 4 years unless you take the precautions I mentioned above.
i'm using a late 2013 macbook pro retina 13" and have replaced my display 4 or 5 times when it was under warranty. today i still face the staingate issue. there's a facebook group about this isssue as well
https://www.facebook.com/groups/607572909386595/