Why does my iphone 6s not wake up for a phone call?
I don't think that I've ever gotten a call on my iPhone 6s while it was charging before, but I can say that some of the little things about the iPhone 6s are buggy, like how some system sounds don't always play.

All that I could recommend is to update to iOS 9.1, as my iPhone 6s is noticeably less buggy on 9.1 than it was on any earlier iOS 9 release.