Is it common for the window seal to come loose and push upwards? If you look at the outside driver mirror, some civic's window seals push upwards to some degree. Is it a matter of taking needle nose pliers and pulling the seal away from the mounting flange and stretching it downward?

 

Have to remove inner door panel and release the rubber window gasket and work it down. It took me all of 45 minutes start to finish. I guess the rubber seal just works itself upwards from the window being opened and closed.