I found this answer a while ago so I thought it may be helpful. Please comment if this works for you :)
How to fix Touch ID Not Working Issue on iPhone 6/6 Plus
Step #1. Launch Settings → Scroll down to tap on Touch ID and Passcode. Enter your passcode.
Step #2. Turn OFF iPhone Unlock and iTunes & App Store.
Step #3. Press home button to return to home screen and then restart your iPhone by pressing sleep/wake button and home button.
Step #4. Launch Settings → Scroll down to tap on Touch ID and Passcode. Enter your passcode.
Step #5. Turn ON iPhone Unlock and iTunes & App Store.
Step #6. Tap on Add a Fingerprint… and add another finger as usual.
With the above steps Touch ID will start working properly