Experienced this bug when running on Mac OS X 10.11.5 in both UE 4.12.3 as well as 4.12.4. It didn’t happen in earlier versions of the engine.
When I close a project in the Editor, the Editor remains open as is visible on my Taskbar: there’s still two icons present for the Unreal Editor processes and also in the Force Quit window the two processes are present. You cannot Force Quit the programs, or rather, doing so has no effect. They do not appear as processes in the Activity Monitor. They’re just ghosting. I haven’t noticed a big hit on performance, so it doesn’t look like the actual editor is still active. Just the closing program is ghosting or some such.
Reproduceable in 100% of the cases where I close the Editor: through the red X button, through the quit menu, through ⌘+Q quit and through Force Quit.
It does prevent my Mac from shutting down, logging off or restarting, however. A hard shut down is required to get the hanging Editors to disappear.
The problem can be avoided when I save a project right before closing it, no matter whether I made any changes or not.
However, if I close the Project Loading window (naturally there’s nothing to save there), I cannot prevent the bug.