Folders may appear to have duplicates because multiple folders have the same Auto-Name, even though the folders are unique based on Keyword or date range criteria. Ensure the Auto-Name strings on folders include Keyword values or date ranges that uniquely identify the folder.
For folders created as part of an auto-foldering process, check the auto-foldering configuration. There may be too many Keyword Types assigned either as required for auto-foldering or as common Keyword Types between a parent and child Folder Type. Auto-foldering uses each of the assigned Keyword Types to determine whether a folder already exists. If a document is archived with a unique value for any of the auto-foldering Keyword Types, a new folder is created.
Only Keyword Types required for a document to find or create the correct folder should be assigned for auto-foldering.