Kaoru makes Kenshin stay in the separate room because he saw her naked when she was taking a bath. He was trying to ask if she was OK but thought she was quiet because she was trying to kill herself.(reason= her last students quit) Also near the end of the episode when Kaoru invited Kenshin to stay with her, he said that he might see her naked again. She punched him and apologized because she thought he could dodge it seeing he is the Battousai.