I started a new course by importing most content from last semester's course. I wanted to leave out some of the files, so I deselected those check-boxes (including the top level, because all of the files should be within the folder structure). But all of those files came through - it acted as though I had chosen to bring everything over.
Just a thought - does the original course have modules in it? If you imported a module that contains a link to a file, that file would be imported as part of the module even if you didn't specifically tick the file when choosing the content items.