Hello,
I have the exact same problem. My Surface Pro 3 is bought in August 2014. I noticed a strange coffee mug like stain in the center of the screen. It can't be cleaned. If I use a paper cloth it disapears, but after a while after using the touchscreen alot with my finger the circle shape comes back.
That's when I searched the Internet about this, and found this forum.
Not sure what to do now. It doesn't seem to affect the touchscreen, and it is not visible when the screen is turned on. However, since this was a € 1500,- euro device I did not expect this.