Why did Aperture just download over 500 duplicates from my camera.

Despite having ticked 'do not import duplicates', Aperture imported over 500 duplicates from my Canon 7D.
Anyone have an idea why this happened? I take it I have no choice but to go through and remove these manually.

The built-in dupe-sleuth is rather dim-witted.  All it checks is file name and the date-time stamp (iirc).  If you change either -- for instance, you rename files on import -- it assumes (not without reason) that the files are different (they are) and imports them.
I just shoot a separator frame each time I put a card in a camera.  (Point at a light source, hold up one hand with a finger extended, and take an out-of-focus shot.  Easy to pick out.  Every exposure preceeding the last separator frame has been already imported.)  Because I _always_ rename my files on import, I could not use Aperture's "Do not import duplicates" function.
Grouping (and then deleting) the most-recently imported dupes is easy.  Select the "Photos" container, and filter for the import sessions that are most recent.  You will have to add the Filter Rule "Import Session".

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