Well, the "good" Kirk was extremely preoccupied with nobody finding out about his "evil" half, even after giving a shipwide announcement about the existence of an impostor. He would probably have been principally concerned with getting the "evil" Kirk out of sight and to the sickbay unnoticed - and right after that was accomplished, Scotty called him.
Remember that not only is Kirk failing to give relevant orders, but Spock is also concentrating all his attention on the hunt for the double and on the effort to protect Kirk's authority, just as ordered by the "good" half. Neither of the two would be concerned with transporters or the survival of the landing party at that point. It's a glaring oversight - but one made by the characters, in character.