Remove whichever one is NOT linked to the Wiki Moderators setting. If you delete the group that is being used, all of your existing wiki moderators might be removed. When you have duplicates, the easiest way to tell the difference is to rename one of them and see which of the new names is still selected in Options > VaultWiki: Miscellaneous > Wiki Moderators Group.
The duplication was "fixed" in 4.0.11. As of 4.0.11, admins were given the option to pick an existing group for Wiki Moderators or to customize the group name at installation.