I recently purchased an iPhone 6S, and the motion tracking worked for a few days, but then in the past four days it has recorded no steps or flights climbed. This morning, the phone started recording data again, but only briefly (maybe 2 hours); it currently is not collecting any motion data. I've been using Apple's Health app and the FitBit app. I tried turning motion tracking off and then back on, restarted the phone, no luck. I'm on iOS 9.0.2. Any ideas?
Try restarting your iPhone by holding the lock button and home button together until you see an Apple logo appear. If that doesn't work, I'd attribute that issue to a bug. The iPhone 6S is kind of buggy, mine won't play system or Taptic Feedback sounds sometimes. So we may just have to wait for software updates.