You can now set up both SMS and an authenticator app (TOTP) for two-factor authentication on your GitHub.com account. Previously these methods were mutually exclusive, and you needed to create a "fallback" SMS registration that could be used for account recovery.
With this update, we are removing the fallback SMS option, and will migrate all fallback SMS registrations to be standard 2FA methods today. A small set of users had both a primary and fallback SMS registration on their account – they continue to have that fallback SMS registration, and will receive email about it today.
To learn more about setting up 2FA and GitHub's account recovery methods, see "Configuring 2FA" and "Configuring 2fa recovery methods"