After upgrading Lion to Mountain Lion on my 2011 15" MBP, I've only seen one issue, but it's insanely irritating. I use an external monitor, keyboard, and mouse while sitting at my desk. Before ML, I could unplug my (Microsoft) keyboard (via a USB hub) and all other USB connections, go to a meeting, then come back and plug everything in just fine.
After ML, and without any physical hardware changes, now when I unplug the USB hub, go to my meeting, then come back to my desk, plugging the USB hub back in brings back all devices (mouse, drives, etc.) EXCEPT my keyboard. In order to make the keyboard work again, I have restart the computer. This works, but is insanely irritating.
I've zapped the PRAM. I've reset the SMC. I've checked for updates to the MS Intellipoint software (there aren't any), and I've run all software updates.