Everything works fine from the start until you kill the cube and 2 spheres, then the shields are dropping on everything instead of needing to keep up constant damage on the gateway. I've played several times now, and it is the same.
What you're seeing is pretty much the entire point of the last fix. You start from the "bottom" and work your way to the top. And the "hard" part is now dealing with the waves of reinforcements that warp in while you're working on the fixed objectives.