Same issue with mine, you can try these:
If the problem still persists, then
https://support.apple.com/en-ca/HT201295do all the instructions
If the problem still persists, then
https://support.apple.com/en-us/HT204063If the problem still persists, then
https://support.apple.com/en-us/HT201262 Third-party apps that may be interfering the startup (startup items are probably at fault) and made the touchID not working properly.
Back to the normal startup, and I tried to uninstall a third-party app (anti-virus), then touchID work properly. I tried to install it again and guess what, touchID still work like a charm!