My problem is a bit like the issue given here: Mouse selects everything on its own except it occurs in both Gnome 3 and Unity. It doesn't happen in all applications though. So far I've observed it primarily in MATLAB (R2012a), Nautilus, Chromium and the Gnome and/or Unity dialog boxes. Essentially I'll go to click something (like to go to a certain location in the MATLAB editor, or to click a button on a system dialog box) and instead of clicking where I pointed, the click is performed somewhere else, perhaps opening another menu or even selecting a large chunk of text in an arbitrary part of the screen. Furthermore, Nautilus recognizes left and right clicks but never at the location I actually clicked. However, dragging works.
It happens whether I am using the touchscreen (HP TX2) or a wireless mouse, or the touchpad. I am on Ubuntu 12.04, and I have also uninstalled Compiz to no effect. If I reboot the problem sometimes disappears, but it either comes back after a few minutes or if I suspend and resume.