Seems like a normal workflow to me. When I import my pictures from my camera, I import them into a "year" project and a "year-month" album. That become their default "location" in Aperture. However as I arrange my pictures, I want to move them into other projects and albums. Because of the way Aperture use projects and albums, this is not an easy task:

I want to move picture P from Album A1 in project P1 to Project P2.

Drag the picture P from Album A1 to Project P2
Aperture will issue a warning: "You are about to move one or more master images to a different project. References to them will be maintained in any album that include them". Click "move".
Aperture will move the master from P1 to P2. Aperture will copy the version from A1, leaving a copy in A1.
You should immediately "remove from album" P from A1 to clear out the old version in the old album.