Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.

I've definitely seen some weirdness with apps downloading, but it's not unique to the 6s line. e.g. I've had apps needing updating, and then the app disappears from the iPhone until it's updated. Just peculiarities. Wouldn't sweat it too much.
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.