Users complaining Google Authenticator keys not working. Ask them to go to Settings -> Time Correction -> Sync now in the Google Authenticator application and try again.
Yubico YubiKeys aren't working. Check you have configured an API key in the two-factor options in the XenForo admin control panel.
Two-factor is enabled by default in 'Your Account' area. This is correct, however until the user adds a two-factor key (e.g by attaching a Google Authenticator) it will have no effect on the login process for them.