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This is a well known issue and relates to problems with replication of data from the Kobo site (either via WiFi or Desktop).
The "Kobo Utilities" plugin has a function to clean the duplicates up; look at the option Database | Fix Duplicate shelves. Pay attention to the "Purge duplicate shelves" button; you probably want to leave this unchecked.
Also as long as you do all management via Calibre it should not matter which option you select for "Shelf to Keep".
There is also an option you can add to the Kobo eReader.conf file to ensure that shelves are NOT synced to Kobo; unfortunately I can't remember it right now.
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