Are you speaking for the .tmp files, there's would be incomplete files that are still cued for DL, the quickest and painless way to get rid of them is to remove the .temp extension and delete(AG always looks for the .temp to resume the DL). i've done this and they've never shown back up... another way would be to remove them from your queue list in AG, although I don't think that removes them from your HD.
Kyfe