Some users register with auto pre-fix username

The prefix can be set to something else if you don't like that format. Just go to JFBConnect backend > Configuration > General area and choose a different option for the 'Auto Username Prefix' setting.

Is there any way to prevent this from hapenning and always force them to put their own username manually?

The option for this is JFBConnect > Configuration > General > Normal Registration section > 'Username Field on Registration' setting.

So how is that hapenning to a small percentage of users?

What do you mean by this? The username prefix is only used when logging in via a social network.
* If you have Automatic Registration disabled, the prefix will be used during all social network logins, not just some.
* If you have Automatic Registration enabled, some users may still need to go through the mini registration process if they're logging in with a social network that doesn't allow for email import (such as Twitter). In this case, you would still see some users with this name format.

-Melissa