That didn't take long at all. The moonroof once again failed to close properly tonight. We decided to give it some more time before we take it back in (i mean we would actually like to have some time with our own car for a change). Maybe waiting a while will give Honda more time to determine how to fix the problem.
Also, ever since we picked the car up there is a noticeable "click" sound every time we press in the brake. Once the brake pedal reaches the point where it disengages the gear shifter to allow shifting out of park, that is where we hear it. There was no noticeable click when we first purchased the car and the Pilot my mother in law bought (based on our recommendation) doesn't make that noise either.