Looks like I have a way to reproduce it consistently:
1. Resume the current quest (doesn't seem to matter what it is).
2. While in the quest/game, switch to Finder (i.e. with Command-Tab)
3. Switch back to D3
4. Click the button to bring up the menu
5. Click on Leave Game
6. Exits D3 instead of just the game.
Mac OSX 10.7.4
Also running Battle.Net desktop beta.