I've noticed this with mine as well and it has been driving me nuts! Turns out I just need to massage the screen for a bit and the dark spots work their way out. After a little time they seem to come back in the same general area middle to upper top and up by the battery indicator. I think all 6's have this and most people don't notice. The display had gotten so thin and I believe it's an edge lit display and this is as good as Apple could make the screen. Hopefully they go amoled next time around.
Install the app dead spotter go to a white screen crank up the brightness and I'm betting a lot of you will see faint shadows that you can move around if you gently push on the screen.