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I've recently set loads of different torrents downloading, many of them are of the same thing (I want to download them all and choose the best quality version).

I have just noticed that some of them appear to be sharing the same download folder! 

When a torrent begins downloading and there's already a folder with the same name, I would expect it to add something like "(2)" after the folder name, to keep them separate, or perhaps add an ID of the torrent. But this doesn't seem to be happening?

Is this a bug, a flaw with the software, or am I using it wrong?

Bump.

I currently have ELEVEN different Torrents all downloading into the same output folder, even though each torrent is a different total size!

If you're downloading multiple torrents into the same download folder, be careful about deleting them!
There's been reports that deleting any torrents using a download folder deletes the download folder even if it's not empty!