I was running iOS 9.0.2 Jailbroken when I replaced my battery. I'm not sure why, but I assume some security feature prevented Touch ID from being enabled again, I tried reseating many times, checking grounds as mentioned in another comment, hard/soft rebooting, nothing worked. Unfortunately my last resort was to restore in iTunes and upgrade to iOS 9.3.1. Touch ID works fine now as does everything else, but unfortunately I lost my jailbreak for the time being.
So before you start, I recommend backing up your phone BEFORE YOU DO ANYTHING and if you have issues after try restoring.