Hi Guillaume, I think that this happens (both doubled surfaces and unjoined pieces) if you try to join together 2 objects where the objects share a common face.

For example these 2 cubes:

If I were to move those 2 cubes together and then do a "join" on them, I think that is the type of situation that is causing this problem.

I should be able to fix this up to work better, but in the meantime you should only join pieces that have open edges. Like for the cubes for instance, I would delete the common face (on both cubes) before trying to join them together.

Do you think this thing (join with common overlapping faces) might be what you ran into?

If not, then there is some other problem that I would to track down, please let me know if you figure out which operation is causing it.

- Michael