It happens at 38:53. What am I doing wrong here?

you can block his pathway sometimes depending on where you stand, try standing on the left side for that last shot like here

oh at 38:46 I think you (or the little headcrab) blocks his path, because gonarch ran in the middle of the arena after the shot instead of straight to the back like usual. So just make sure for all 3 shots that you go where Kananga does them in the video. I'm not sure if the small headcrabs that gonarch spawns can block his path, so just make sure to charge the gauss and shoot earlier so he doesn't spawn any I guess.