According to posts made on Apple’s Support Communities, it seems that there are some users who have had Touch ID stop working or malfunction after the update. According to these users, the update has either made Touch ID slower to recognize fingerprints, or fail to completely recognize fingerprints.
One user writes, “The Touch ID was working normally before installing IOS 9.1, then after the restart and after entering low power mode, it stopped working,” while another claims, “I’m using an iPhone 6S 64GB and upgraded to iOS 9.1 a few days ago. My Touch ID has become very slow or either doesn’t work after several attempts, and I need to input my passcode.”
It is unclear as to how widespread of an issue this is. I personally have the iPhone 6 Plus with iOS 9.1 installed and Touch ID works fine. We’re not sure what is causing the problem but it is apparently serious enough where a hard reboot doesn’t fix it, at least not permanently. Hopefully this is an issue that Apple will sort out soon, especially when you consider Touch ID being a rather prominent feature of the phone.