I am 20k miles into a 2007 hch and notice a really annoying rattle coming from the left side rear door. Its a quiet rattle but noticable, especailly when you go over some light bumpts on the freeway it will set up like a buzzing sound, or like a ball bearing thats loose. I have an idea that its related to the window opening mechanism but not sure.

Anyone else had this?

Let the dealership have a listen? Has it rattled thus since new? Apart from misaligned door, might be a popped out (or misplaced during intitial assembly) fastener.

Does the door sill show any wear points, ie: points of contact with the door? I think the rubber stops are capable of being screwed in/out a bit, to adjust fit. You might try turning them out slightly, see if it changes anything.