The rear HVAC unit in the Ford Expedition is known to cause a knocking, ticking or clicking sound when the rear heater or air conditioner is activated. 

 

This is caused by a faulty blend door or blend door actuator, which changes the temperature of the air that comes from the vents, so the issue may also be in conjunction with an inability to control the air temperature for the rear vents. 

 

Replacement of the blend door actuator is typical, but the blend door may need replacement as well.