That is the safety stop. The controller will autofill until water reaches the predetermined level. If the controller senses that the current fill is 3+ minutes longer than the previous fill, it will automatically shut off the pump regardless of water level and will sound an alarm letting you know that there is something wrong.
If the controller has a air bubble trapped in between the magent, it will sound an alarm. If the controller has algae growth that prevents the optics from working correctly, it will sound an alarm. if the controller senses that the pump has been running dry, it will sound an alarm.