If you've had any warnings about it they likely originate in it's use.
If you use uTorrent to download legitimate torrent files (Linux distributions, games, applications for the originators websites) you'll be fine. But if you were to use the same tool to download from illegal file sharing sites then all bets are off and you could be downloading anything.
mrplow is correct - the application itself should be fine but what you download with it is another story. Keep your downloads clean & legal and you should be fine.
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