When the heater is turned on, it makes a knocking sound that is loudest from this hole on the outside. The heater is turned on from a thermostat inside.
Looks like intake and exhaust, like Neal said, could be expansion and contraction. Check any screws you can access and snug them up. What kind of noise? Can you describe it? When running, the lower opening, most likely, is intake for combustion air. Upper opening is exhaust and you should feel heat from it when on?
If this happens just after the heater is fired up, my guess is there is a metal expanding going on. Does it stop after it has heated up, or just continues?