If I add a node to a scene, and then click the editor's close box, I get a popup dialog with three buttons: Don't Save, Cancel, and Save & Close. If I then click outside of the editor, causing the Godot editor to be hidden, and then click the Godot icon in the task bar, sometimes the main editor window appears, with the popup dialog hidden.
In that situation, the editor window appears to be frozen. I have to Alt-Tab to get the popup dialog so that I can click one of the buttons. Then the editor window behaves normally.
That's happens with other apps that can have modal popup windows.
That's the closest that I can get to the problem you described.