The touch ID on my first iPhone 6 was wonky right from the start as well. It would work for a while, and then stop. And for a while, I mean less than a day. I used different fingers and ended up with the maximum number of fingerprints entered and I would quickly get to the point where none of them would work. Then I would delete them all and start over again. I figured the issue was my fingerprints. I wash my hands frequently and my skin gets dry, so I always thought that was the problem. My spouse, also with the iPhone 6, has never had an issue with his.
Other issues developed with the phone, which ultimately ended up being hardware and the phone was replaced 4 months after I bought it. Hardware issues involved the wifi antenna, which died a slow death until it quit entirely, and the bluetooth, which died totally along with the wifi. At the time, I didn't connect the touch ID to all of that, but after having replacement phone #2 and having a properly functional touch ID for the first time, I do think my touch ID was faulty from the start. As it was with phone #2...although I was still blaming dry skin.
Yesterday morning, when I woke up, my phone asked for the passcode. I thought it had restarted during the night. This is what my first defective iPhone was doing when the hardware issues started, so I was alarmed. But now that I think about it, I don't recall seeing that message on the screen, only that the passcode was needed to enable touch ID. My spouse says his does that every couple of days or so as well, so I guess it's not a big deal. My other two iPhones never did, probably because I had to reset the touch ID so many times that it never had the chance.
It looks to me like the whole touch ID technology still needs some fine tuning.