It is a bug, I don't know the number.
The unified folders are actually saved searches, you can right click
them, choose properties. and then choose from what folders messages are
to be displayed. Sometimes it doesn't work the way it should, possibly
because you started using Unified Folders when you still had only one
account configured. The Junk and/or Trash folders become "real" folders.
What you have to do is close Thunderbird, go to your profile folder and
delete Junk, Junk.msf, Trash and Trash.msf from the "smart mailboxes"
folder. Restart Thunderbird and everything should be alright, the Junk
and Trash folders are automatically recreated.