Duplicate files on the computer, or duplicate entries in the iTunes window?
Unless you have changed preferences settings or are doing something non-standard with iTunes an iTunes folder will contain a separate stand-alone library. You can have dozens of them if you wish. Opening a new library does not merge or duplicate content with another, and certainly not in the the iTunes window itself. There may be a separate component coming into play here such as automatic downloads from the iTunes Store which is not always very good at identifying content already in your library if you have been altering the tags/labels.