That can happen a few different ways. It's not common, and it usually only happens under development / testing environments because in that mode, you'll be switching between accounts, tabs, and Facebook sessions. There's not a bug in JFBConnect, it's just a matter of how you use each of the tabs that can cause an account to get re-linked.
Basically, when user A) logs in, but is logged into Facebook with a different account than they have connected to your site (or no account mapping at all), the SCLogin module will have a link that says "Connect this account?" If you click that while logged in, it will update the current user's mapping to the new Facebook account, replacing the old mapping. You can disable the "Connect this account?" button in the SCLogin module for "Allow Reconnections".
Additionally, if you are switching emails for the Joomla user that is logged in, when the next Facebook login with the same email address, the Joomla account with the same email address will be remapped to the Facebook account.
So, in short, there are a few uncommon ways that accounts can be mixed up. It's almost always a case of it happening in test environments, and it's always from an unintentional click or change in user settings. There's no reason JFBConnect will remap a user without some intention of it happening. If you notice a case where it does happen unexpectedly, let us know what happened on that page load.
Thanks,
Alex