I encountered this issue when I played Call of Duty 4 Multiplayer on my Mac today - in full screen mode. Upon launching the game the microphone is activated and Micro Snitch's overlay appears. When switching out of the game by pressing the CMD+TAB keys, the overlay is slightly offset - it does not automatically adjust to the correct corner position. You need to manually drag it a bit for it to snap into the right corner position again. I'm not sure whether this issue also occurs with other full screen applications utilizing the microphone, but I thought it would be worth it mentioning this.
Here is a screenshot of the misplaced overlay right after I pressed CMD+TAB to switch from the game to Finder:
General discussions about Little Snitch
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