While downloading a TV series that all download to the same directory when one finishes it copies the root directory for the download and takes the other downloads with it and then the downloads complain that they have lost their files.

Example:
Torrent A:
MainDir/Ep1.avi
MainDir/Ep2.avi

Torrent B:
MainDir/Ep3.avi
MainDir/Ep4.avi

Torrent C:
MainDir/Ep5.avi
MainDir/Ep6.avi

When Torrent A finishes downloading and the files are set to move to the directory for finished downloads it takes all of MainDir leaving Torrents B,C, and D to wonder where their files went.

Possible fixes (among others) could be to recreate the directory structure of the torrent in the destination directory and then move files and delete directories only if they were emptied out, or check in the final downloaded directory for files that may have moved.

At this point it is more frustrating than anything but I'm fortunate not to have many files to move each time, I pity anyone who has to move a few hundred unsorted files after something like this.

Version ?

Ahh, sorry about that, I'm on version 2.2.1, the version in the kubuntu repositories, I'll go update and try to replicate it.

This is now fixed, the fix will be part of 2.2.3