On some models the drivers and or the front passenger door glass will come out of it's track. The door glass will have to be replaced to address this issue.Google+
Car Problem Reports
Honda Civic Si Front door glass off track
Honda Civic Si Problem
Visitor, 2007 Honda Civic Si
My window was partially down, I had shut, not slammed the door, and the window became not much but visibly off track. I pulled the window up a little with my hand and it went back to where it should be.