There are some adjustments to be made. I replaced my window glass guides recently and put it back together and the bottom was out of line...
Take off the door trim, two screws at the top at each corner, one screw behind the handle inside the car that removes a plastic cover that then exposes another two screws. Carefully ease the door card up and then out slightly, you will then need to unclip the handle mechanism cable, and all the wiring clips(speakers window switches and central locking) you will see which ones to unplug when you look behind the door card.
Door card off... the top half of the door including the window glass is bolted to the bottom using 4 torx head bolts, two at the top two at the bottom. From here on in is trial and error untill yours lines up properly. I loosened all the bolts slightly to allow a little movement. You will see that the bottom bolts have a aluminium wedge between the bolt and door - this is your adjustment, mine was a case of moving the wedge down a little on both sides. Do the bolts back up and see if it fits.
Hope this helps