Not clones but physically identical. Agent Barnes did not appreciate the ambiguities of this place. To Agent Barnes, the world was black and white. There were his orders and there was everything else. And if he asked questions, he got answers--or he got reminded why they didn't go asking questions in the first place.
He took Jefferson's words at face value; if he was being lied to, it was for a reason, and if he wasn't, then it was the truth, and that was for a reason too. But Jefferson also clearly was not aware of Agent Barnes' reputation. This incident aside, he was not a problem agent. He wasn't even properly an agent. He was an asset, and he simply did his job.
"With respect, Agent Jefferson," he said, "I don't cause trouble."
He nodded at the incompetent agent, to show he could understand his orders and knew exactly what his job was now. "Until my assignment in Marrowood is complete, I am Agent Barnes and Agent Jefferson is my handler. Unless given specific orders, I'm not to shoot anyone. Any mission orders will come from you or Agent Jefferson."
Maybe repeating was a bit excessive, but--well, Agent Barnes was positive of his own faculties and what he could and could not retain, but it might have benefited the incompetent agent to hear it repeated. Reassuring, one might even say.