Duplicated content on homepage
You have to delete those duplicate alias by going to the alias list at admin/config/search/path (in Drupal 7). It's not an automatic task, I'm afraid.
Or you can delete all alias and bulk recreate them using the Bulk Update function. That would be an automatic process.

As a last step, you should check Alias Settings at admin/config/search/path/settings. I think you should change the "Update action" to "Create a new alias. Delete the old alias.".