Why does Aperture duplicate my raw files?

I downloaded the Aperture demo a week and a half ago and started working on some photos which were on my hard drive. There was an enclosing folder with the name NAfricaSahara, and then within that folder 22 folders organized by date. There were about 3200 photos altogether.
Now after working with about half of the raw files in Aperture, I have found that most of the raw files have been duplicated so that they are now loose in the NAfricaSahara folder as well as within the 22 date folders. This includes files I have worked on as well as files I have not worked on. Is this normal behavior for Aperture? I put one of the duplicate files in the trash (the original still was within its original date folder) and it disappeared from the Aperture window.
How do I prevent this from happening? The duplicates are really eating up a lot of my disk space.

No, I haven't copied versions. What I did was import the NAfricaSahara folder into Aperture. It contained subfolders by date of download to my Epson 4000 digital wallet. The subfolders also came into Aperture as Albums.
I then moved some of the photos by selecting them and creating new albums (in cases where I had downloaded to the Epson less than daily) so that there was a album for each day.
What I see in the Finder now are all the original folders I set up along with their contents. But all the individual files are now ALSO in the NAfrica Sahara folder (not in any subfolder), as well as in their original sub-folders.
I don't want all these duplicates, but when I try to trash one, it disappears from Aperture.

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