I think I've got this problem of duplicated surfaces fixed for the next beta.

It would happen if you joined 2 objects where already-joined edges were touching (as in the 2 adjacent cubes example above).

This would create a situation where more than 2 surfaces were joined together at an edge, which confused some other things later on which result in duplicated surfaces.

Join has been improved in the next beta so that it only tries to join open, unattached edges to other unattached edges so it won't end up creating this type of messed-up object.

- Michael