i noticed this, i dont know whether its to do with the rubber, but i usually detail the top and sides quickly, then fan the window, overlapping where ive just been, usually there are no marks but if the windows are quite wet from scrubbing with the tbar, then this sometimes happen - then i quickly go over the top and sides with a cloth and dry the end of the channel both sides by quickly rubbing in the cloth- this has become habbitual and then squeegee straight down the window, overlapping and it leaves no marks.
once you get the hang of it, its really quick and if you do get the lines, then quickly go over it.