My passenger window glass broke a coupl eof weeks ago for no particular reason, when car was standing in the garrage. I just ordered it from Mercedes as it was less expensive then in some of the internet stores (tinted with guiding jaws, ca EUR 350) and I did not have to worry about shipping, which in case of glass may be important. It is back in its place, I just need to finish adjustments.
And adjustment, I think, might have been the cause of your issue, based on your description. You might have had too much tension on it in closed position. I am not sure when the glass should push through anything, any molding or seat. It should be closing nice and easy with no tension, I think.