Deluge
I was downloading several torrents sharing the same root folder
torrent1: series_name/part1.avi
torrent2: series_name/part2.avi
...
so in the active torrents folder I've got a folder series_name with files part1.avi, part2.avi and so on in it. An option to move completed torrents to a different folder was on and when the first torrent finished downloading deluge moved the whole folder series_name with all files in it including files which where still being downloaded as parts of other torrents. When moving torrent storage deulge should not move the root folder of the torrent but create a new folder structure, move files one by one and then remove empty foders in the source tree.
rc5, ubuntu hardy 64