I see what you did here.
Since I couldn't find a good enough pic of the sniper, I went with the same one, different style
If you notice, the top part doesn't automatically round out into there.
1. Extrude the bottom polygon of the top cylinder, shorten it until it reaches maybe a theoretical inch to the sniper.
2. Extrude again, bringing it all down
3. Take the front part/edge of the extruded cube, and bring it forward to the barrel.
That should fix the problem.