Not sure why it's happening, but the utorrent script is misidentifying which episode is a particular Real time with Bill Maher episode. I assume it is something going wrong with the identifying the date in the filename. Here's the the relevant log:
Input: /home/belgarth/Downloads/.torrents-download/Real.Time.with.Bill.Maher.2013.02.01.720p.HDTV.x264-EVOLVE/real.time.with.bill.maher.2013.02.01.720p.hdt\
v.x264-evolve/Real.Time.with.Bill.Maher.2013.02.01.720p.HDTV.x264-EVOLVE.mkv
...
Auto-detected query: [Real Time with Bill Maher]
Fetching episode data for [Real Time With Bill Maher]
...
Include [Real Time With Bill Maher - 11x03 - February 1, 2013]
...
[COPY] Rename [/home/belgarth/Downloads/.torrents-download/Real.Time.with.Bill.Maher.2013.02.01.720p.HDTV.x264-EVOLVE/real.time.with.bill.maher.2013.02.01.\
720p.hdtv.x264-evolve/Real.Time.with.Bill.Maher.2013.02.01.720p.HDTV.x264-EVOLVE.mkv] to [/home/belgarth/Downloads/TV Shows/Real Time With Bill Maher/Seaso\
n 1/Real Time With Bill Maher - S01E02 - February 28, 2003.mkv]
[COPY] Rename [D:\testdata\AMC-TEST\Real.Time.with.Bill.Maher.2013.02.01.720p.HDTV.x264-EVOLVE.mkv] to [D:\output\TV Shows\Real Time With Bill Maher\Season 11\Real Time With Bill Maher - S11E03 - February 1, 2013.mkv]
I assume episode data was not available at the time, either because it wasn't in the db yet or previously cached episode that has not expired (though it's only 2 days with the latest release).
EDIT: Huh, really doens't work with 2.4 ... well, can't be bothered, works with the latest HEAD.
Please read the