c35505c created the issue

After clicking a menu item (most recently, the "Cyberduck Help" item under Help). This item stays in a semi-translucent state on the screen in the original position in which it was clicked.

It also doesn't disappear when Cyberduck is closed.

I've taken a screen recording here: https://gfycat.com/ShockedPlumpCockroach

The only fix I've discovered to remove it from the screen is to restart the computer.

Edit: after further research, the phantom display can be fixed by changing the screen resolution temporarily (or otherwise restarting the Desktop Window Manager). More info: http://superuser.com/questions/57016/menu-select-item-stuck-on-screen-after-context-or-command-menu-has-closed