Having been in the automotive glazing industry for the last 20 years , this i am afraid is a common problem,
Firstly, You may have a degree of adjustment from the motor and may be able to re adjust it to go up more square by loosening it off and moving it about to find the best position for it to operate smoothly.
Secondly if its the drivers side its gone up more times and the scissor mechanism may be very worn and may have a tendancy to allow the whole mechanism to be jiggled about and this allows the glass to go up at a slant,
Thirdly , if you cannot get any new rubbers try greasing it up so the glass does not dig in the rubber and cause it to cock over,
Fourthly , do not force the glass up as you may go the wrong side of the rubbers and you may break it , just assist the glass up by holding it square in the door, if you strip the door panel off , a automotive glazing company will give there advice on it freely and point you in the right direction .