1. A user logs in with Facebook (first time registration) and then subsequently registers with her email.
2. A user registers with her username and email, and then at some later point logs in with Facebook.
Does JFBConnect know it’s the same person and therefore have only one Joomla account, or are two user accounts created for both use cases?
If the email in Facebook for user in #1 matches the email that user #2 attempts to register with, Joomla prevents the registration as email addresses are required to be unique for Joomla accounts. My guess is what happened is that you the emails for #1 and #2 do not match, so a second Joomla account was created. Any log in with Facebook credentials will map those credentials to the Joomla account with matching email address if you have the "Automatically Link Users by Email" option enabled.
-Melissa