Extra Copies of photos

In my Pictures directory I have found some directories of photos alongside my Aperture library. I decided to move them out as I have them already on my external drive. After carrying out another import on Aperture some of them are back. Any idea why Aperture would do this?

Maybe I didn't explain properly.
I have originals on my external HD. In the pictures directory of my internal HD is the Aperture library. Alongside this are folders that appear with copies of my photos in. I removed the photos as I didn't want them taking up space. After doing another import into Aperture the duplicate folders returned.

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