This is a common scenario: Your single articles show a duplicate breadcrumb when the article doesn't have an associated menu item. Typically the first one is the menu item for the category blog menu item that the article would fall under. The second is the category itself.
The reason this happens is that the conditional statement in the template for mod_breadcrumbs checks to see if the LINK of the previous breadcrumb is the same as the LINK for one it is generating. Since those items I mentioned have different links, it doesn't see them as duplicates. You have to add the condition to see if the NAME is the same as the previous one. To fix this,