OK, I know I've seen a solution to this somewhere, but as you can probably guess, a combination of search terms like ubuntu windows desktop give so much noise it doesn't seem to matter what I add to those words - and I can't figure out a way to describe my problem without them :P
The issue is that windows docked to the left or right half of the screen (using either click-and-drag to the screen edge, or Ctrl+Win+arrows) "overflow" into the neighboring desktop (see screenshot below). This means that this window shows up in the alt-tab rotation, constantly causing me to focus on the wrong window, and also that I sometimes push the wrong window to a neighboring desktop when I move around.
I am running Ubuntu 12.04, with a 2-by-2 desktop configuration. I do not use CCSM (and I don't want to). I'd rather just dig down in the config files by hand if I have to (and I have clear instructions on exactly what to do...).