What is your Aperture version?
i am not really sure, if I understand the problem correctly. Are you saying, that the stack shows the wrong items in the stack? Is this in the Browser only, or also in the Viewer?
If you see apparently wrong images and suspect a problem with the referenced images, try to toggle between original master and version: select an image and press "m". Then you will see, if the thumbnail or preview is referencing the correct image.
- If the thumbnails in the browser are not correct, select the images in the browser and use the command "Photos > Generate Thumbnails" from the main menu bar,
- If the previews are wrong, use "Photos > Update Preview" or hold down the "⌥" key and select "Photos > Generate Preview"
If none of this helps, use the "Library First Aid" to repair or rebuild the Library.