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There should be 2 adjustable cloth covered bumpers mounted on the door which can be seen once the door panel is off. Yours are probably out of adjustment or missing.
I get a rattle, most noticeable when closing the door with engine off, on the driver's side only. Been told it's the "bumpers" and a simple fix; just remove the door panels and switch out for new replacements (do passenger side, too). Haven't yet because it's not too big a deal. When/if you do yours, could you post a pic showing us?
Yes, they are what he was talking about. However, there are other factors you won't be able to see until you remove the door panel. One you can see is the "wiskers" at the top of you door panel and outside of the car that the glass slides thru, check the condition of them. The others could be loose bolts on the channels, so that the whole thing is moving, or loose /broken tabs on the electric motor mouting, if you have this. Hopefully you have overestimated the distance you can move them as that is more than they can adjust to If you have a factory service manual, it is easy to do, if you decide to totally remove the channels, etc. to clean and re-lube, be sure to mark their position before you remove them, as the window adjustment can be time consuming.