If you're referring to the channels on the sides of the rear window, yes those are supposed to be empty with no rubber in them, have been like that forever, every Civic I've owned was like that. The only channels they put rubber in is the sides and top channel on the front windshield and the bottom of the rear window. Makes sense they don't have rubber around the rear window, water flowing down from the roof hits the horizontal drain channel on the top of the rear window, moves either left or right and then down the side channels. If this doesn't happen due to clogging, water runs right down the rear window like a waterfall which distorts rear vision without Rain-X. If it's going to allow water to run down it's going to allow debris to run down too, just nature of the beast.
If you think that debris in your picture is bad, try parking under trees for a while. Whenever I wash the car I always make sure to shoot the water directly into those channels. Since the debris accumulates by rolling down the channels from top to bottom due to gravity and water flow, I shoot the water in from the bottom up (trunk to roof direction) starting where the trunk lid meets the channel, to "backwash" and watch the little bits come flying out the top. Also the top channel above the rear window too, stuff gets stuck there too.