I had this problem originally but then I had my logic board replaced, then I got it back and when they fixed that they cracked the bottom of the case because they used too long of a screw and THEN I got discoloration.
However after they replaced the bottom case and bottom top case plastics I no longer have this issue, so I really think it is something to do with maybe the spacing or just how it is pressed together.
Talk to Apple, I was mad at first about my case getting cracked but I went to the store and they were very nice, I was polite with them they listened to my problems and had all of my complaints fixed for me.
However after they replaced the bottom case and bottom top case plastics I no longer have this issue, so I really think it is something to do with maybe the spacing or just how it is pressed together.
Talk to Apple, I was mad at first about my case getting cracked but I went to the store and they were very nice, I was polite with them they listened to my problems and had all of my complaints fixed for me.