Yep. I'm on my second 6S now. After about ten days of normal use, I noticed very fine scratches in the center, about an inch from the top. I've owned the 3GS, 4S, and 5S before the first 6S I returned. None of my previous iPhones scratched like this so soon, or at all over two years, without screen protectors. So, I took it into the store last Thursday, and the two reps that helped me had one look, and kicked me a second 6S, no questions asked. Both said "that's not right". Well guess what? Five days later, and this second 6S has a couple scratches now, too. One near the top left corner. One in the center, an inch above the home button. This one, like the first, has only been in cotton lined pockets (always by itself), or face-up on tables, or in my hands. Being that I've been extra conscious of this second one, I know I've done nothing to abuse the screen. Zero carelessness here.
So, now what? Get a protector for the third that will be in my hand in a couple days? F that. They don't feel the same, and are prone to peeling up at the edges. And, according to Apple, and Apple reps themselves, protectors "aren't necessary" (see any Apple brand protectors? ya don't).
What ever glass / glass/coating they're using now, since the 5S, it's either not as durable against fine scratches, or this first batch is simply defective. But, researching iPhone 6 stories from about a year ago today say otherwise to this being a batch defect issue.
Have a close look at your 6/6S'. I'm sure you've got scratches going on, too...