Started getting this clunking sound from the tailgate and thought for sure it was the latch. So, I had the dealer check the latch and adjust it. They did what I asked but the noise was still there. I discovered the inner black plastic panel can move a little at the bottom of the door. When I pushed on the plastic at the very bottom, I heard the clunking sound. The dealer was going to take the door apart and install some foam. I didn't like their proposal and drilled 4 holes and anchored the plastic at the bottom. Looks good and the noise is completely gone.
BTW.....I do not have the automatic open/close hatch and I suspect that constantly pulling down on the black plastic handle to close the hatch had something to do with the rattle developing.
The pic shows one side of the door bottom with two of the screws.