The problem with Bucky's brain is that is had been messed with more than once already. He had already had the delicate pathways of neurons attacked over and over by HYDRA, he had been wiped multiple times and then struggled to recover who he was. So the attack by Rhys was pulling on already damaged material.

Pain blossomed behind his right eye and quickly spread across the rest of his head. His thoughts became a disjointed mess, a wash of red mist and an instinct just to survive. He bellowed in agony and a refusal to yield. Blood trickled from his nose, but he didn't fall, he didn't succumb. He fought through it to fire again.

This time it was no compromised shot, he wasn't aiming to incapacitate, he was aiming to kill.