Water in the doors, is this common? Options

[crandsberry]

So im sitting in my 97 hatchback, it's raining pretty hard, and im watching water roll down my door window and INTO MY DOOR.

Is this pretty common? Why is that rubber trim piece along the top of the door not sealling to the window, is it the window's fault?
The the guy who owned the car before me was kind of a goof, he put thick carpet padding in the doors for sound deadening (maybe he was on to something ) which i took out. Could that have bent something out of wack?

thanks guys