In Settings > Touch ID & Passcode, tap on Finger 1 and then tap Delete Fingerprint. Do the same for Finger 2 and then Add Fingerprint. I'm not sure if I understand your question but if you mean you only set up 1 fingerprint, I don't have an explanation for that. It would be another good reason to delete both and start over.
Note that it is possible to set up the same finger twice and it will then show as finger 1 and finger 2.