Just like in iTunes with your music and iPhoto with your pictures, in Journler your entries may be placed in more than one folder. When you drag an entry to a folder the entry is not moved to the folder. Instead, the entry is added to it. In a sense folders don’t have any real existence. They are simply a way for you to group your entries, with the entries potentially belonging to more than one group.
For more information about folders have a look at the Folders Help page.