I've actually thought this happened to me once.
I could move units about, but I couldn't get any dialog box to work or the end turn button. Eventually, I hit tab to go through all my active units, and suddenly one of my units moved, a dialog box popped up telling me I had learned a new spell, and then every single button click I had done proceeded to come up one after the other.
Save game actually reproduces this issue is in my dropbox. If you try to hit end turn right after loading this guy, it won't do anything. Tab through the units, and move them about, and it will suddenly free up. The issue all began after a pack of wolves attacked my capital, beat the occupying army, and... retreated? Not sure why my capital wasn't dust, but I didn't complain too much.
http://dl.dropbox.com/u/7804175/blah.EleSav