Tagging gone havoc

On my new Mac, I started tagging files and folders to have quick access. When accessing those tags in Finder, however, some folders/files appear twice and they are not always duplicates, i.e. one tagged folder might have 10 items and the same tagged folder that appears has only 9. That lets me to believe that Finder shows me the tagged local files/folders AND the same files/folders that are on my external drives (Time Machine and Carbon Copy Cloner). How can I set it up that only the files/folders on my local drive are tagged?