i have this same problem intermittently. My solution is easy, I will either run the moonroof through a full cycle, opened and then closed and then open and closed again and that usually sets it back into place or...I use the venting setting to lift or raise the rear of the moonroof up and then down until the rattle is no longer occuring when I use my fingers to push the rear edget of the roof up and let its weight bring it back down.
If you are getting the rattling noise while you're driving or not, you can push up on that rear portion of the moonroof and you'll feel the ever so slight movement and hear a faint rattle noise, by using the vent setting you can take up the "slack" as it were, and hold it from vibrating,a simple solution-simpler yet is to do what my Dad says to do, slide the sunroof cover shut and turn up the radio!