When a world loads, and you enter full screen using the OSX full screen button (on the window frame) the mouse may not hide. In this case the mouse and game cursor appear in different locations, and the mouse can still trigger (e.g.) the Dock while clicking the game cursor. When this happens left-clicks are ignored by Minecraft unless you use double-clicks.

The game does not show this behaviour after minimising, and then returning to full-screen.