i've done three EK civics in the last month at work. it's a common problem when the runchannels move. the hardest part is honestly putting the window back in the runchannels. everything else is almost routine.
i can't find pics but you need to adjust the run channels in closer to the window. this will require removing the door panel, loosening the nut at the bottom of each runchannel, pushing the channel towards the window and tightening the bolt back down. also, a good clear silicone spraying (one with the little red hose like wd-40) of all the runchannels helps to ensure smooth window operation (it's part of out services at the dealership to lube all the runchannels
i know it's not the best explanation but it's pretty self-explanatory when you have the door panel off and see where everything is and goes :TU: