Just got another occurrence, and was able to notice a few important details. I had a gnome terminal open, and was unable to click anywhere except in the gnome terminal window. Click-drags in other part of the screen highlighted text in the terminal, so I can confirm that the terminal window seized mouse focus and wouldn't release it. The only way I could recover was to kill the terminal process.
Just got another occurrence, and was able to notice a few important details. I had a gnome terminal open, and was unable to click anywhere except in the gnome terminal window. Click-drags in other part of the screen highlighted text in the terminal, so I can confirm that the terminal window seized mouse focus and wouldn't release it. The only way I could recover was to kill the terminal process.