I would suggest that you turn off Touch ID to clear out any stored fingerprints, and then turn it on again and re-enter fingerprints. Perhaps the day that you initially stored finger information your hands weren't clean, or perhaps you've added a screen protector since then that makes it more difficult for your finger to contact the sensor. In any case, you'll probably do better with a fresh impression. Also, some people just have more problems with Touch ID than others; if this applies to you, sometimes you can improve your odds by storing the same finger in multiple slots of the Touch ID database - the firmware doesn't really know or care if you give it different fingers when adding another fingerprint.
If this doesn't correct the problem it is probably time for a visit to the Genius Bar for service.