If you see a duplicated copy of a sub-folder appearing at the root level, this copy may have been created when the folder owner moved this folder. Or this could happen when a user is invited to the sub-folder first, then the root folder. You can tell whether it is a duplicated copy by clicking into the copy at the top level and look at the file path.
For example, if "Folder Aa" is already a sub-folder within another root level folder, the file path would say "All files >Folder A >Folder Aa". In this case, you may go ahead and remove yourself as a collaborator from the duplicated "Folder Aa" at the root level, so that it does not appear at "All Files and Folders" anymore. To do so, simply click into the copy showing up at the root level, hover your mouse over your name on the right-hand side under the list of collaborators, and choose “Remove” from the “Access level” drop down.
Please do so ONLY with the copy showing at the root level, so that you are only removing yourself from the duplicated copy of “Folder Aa” but not the original copy residing as a sub-folder in “Folder A”.