If you use a remote mail account that also has Junk and/or Trash folders on the server you might face duplicated folders in Evolution.

You can easily tell the two Trash folders apart by looking at their icons. The Evolution Trash folder has a special icon whereas the other physical Trash folder looks like any other folder.

By default, Evolution's Trash and Junk folders are Search folders. They do not really exist but simply display all the messages that are marked as junk or for deletion in any folders of that account.

In order to only use the folders for Junk and Trash on the mail server, select the corresponding Use a Real Folder option under EditPreferencesMail AccountsEditDefaults. In this case, Evolution's local virtual folders will not be used.