Bottom of the window there is 2 metal plates where the window sits in it and the rear one has a stopper on one end so when the windows goes up it hits the stopper and stops there but what happen is : the window is not glued to the plate anymore so when the stopper hits the stop thingy it's twisting( pivoting kind of ) and pushing the window even higher.
Remove the inside or the door ( plastic ) and run the window up end down you'll see what I mean , I have the same problem , I tried to glue it but I need to remove the previous stuff before and it's a pain of the butt to do so I never force my window up , just push the top of the window down it will sit right back in the slot but as soon and you will bring the window up and hit the stopper it will do it again , I'll fix mine one day but for now it's no big deal just do like I said and you'll be fine.