To whom it may concern: I solved the issue by manipulating (not deleting) the doubled DB entry. In the wp_bp_groups_members table, I manually set both the group_id and user_id fields to high values that have no corresponding real equivalents (group, user). Think this now orphaned row won’t do any harm and as far as I can see, the searches like “groups of this user” or “users of this group” result in what I want now.
@3sixty: I experienced exactly the same misbehaviour in my blog = invitation sent, membership requested by the blog member, confirmed twice somehow and… boing, 2 memberships of the same member in a single group.
Is it still there in your blog or could you fix it?
I wonder if it was sufficient to simply delete the doubled/second group-member-relation entry from the MySQL wp_bp_groups_members table? Or does this have any negative side effects?
A more gentle alternative could be to set the group_id field of this entry to a non-existing group 999 or so. Shouldn’t do any harm unless the 999th group is created and an uninvited member pops out of nowhere…