Create a workspace containing only a single maximized window. Restart gnome-shell, navigate to that workspace *via the keyboard*, then go into the overview, and mouse over the window. The top of its close button will be clipped by the edge of the workspace area. But if you leave the overview and come back it will be correct (because the window will be drawn slightly smaller than it was the first time).

Depending on window layout, this can sometimes be seen on workspaces with non-maximized windows as well. This only happens with the first workspace that gets drawn the first time you enter the overview.