Sometimes, if the overview thumbnails order doesn't exactly correspond to the window z-order, the windows might be ordered wrong while closing the overview, and then snap back to their correct order afterwards.

gnome-shell 3.7.5-259-gdf3872f (but I've been seeing it for a long time)

To reproduce,

1) Position two windows like this (smaller window is focused). Programs used don't matter.

   ├─────────screen width──────────┤

   ╔═════════════╗─────────────┐....   ┬
   ║             ║             │....   │
   ║  gnome-     ║             │....   │
   ║   terminal  ║             │....   │ screen
   ║             ║ chromium    │....   │ height
   ╚═════════════╝             │....   │
   ....│                       │....   │
   ....│                       │....   │
   ....└───────────────────────┘....   ┴

2) Open the overview. The larger window will be displayed first, the smaller one second.

   ┌───────────┐
   │           │
   │ chromium  │  ┌─────┐
   │           │  │ g-t │
   └───────────┘  └─────┘

3) Drag the smaller window, move it a little bit, but drop back to its original place.

4) Close the overview (with Esc).

Expected result: Windows always retain their real z-order (smaller window on top, large window below.

Actual result: During the overview close animation, the large window is displayed on top. After the animation, it jumps back to below the smaller one.