I've replaced several of the plastic guides in the windows of my 300SD over the years, and each time I R&R the regulators I'm amazed at the amount of inner door flex I see as I test the repair prior to buttoning up the door panel. Some flex seems to be normal (mine's going on 18 yrs.) but I'd check the channel alignment and "stop" to make sure that misalignment isn't over torqueing the mounting bolts. Of course it could have been just loose nut causing it to "rub" through.
The Golden Rule
1984 300SD (bought new, sold it in 1988, bought it back 13 yrs. later)