Some people get into a huge bookmark mess when they want to merge and sync their bookmarks via iCloud. This is how I finally fixed my issue.
- Turn off iCloud bookmark sync on all of your devices except the Mac, choose to delete all previously synced bookmarks
- Create a backup of your current bookmarks on your Mac, they are located in: ~/Library/Safari/Bookmarks.plist.
- Correct your bookmarks in Safari on your Mac, make sure everything is the way you want it to be
- Create another backup of your Safari bookmarks
- Delete all bookmarks in Safari on your Mac and wait for iCloud to catch up
- Move your bookmarks backup back into the Library folder and wait for iCloud to catch up again
- Turn on iCloud bookmarks sync on your other devices