Actually, her reaction is related to Jiyoung, right side, having a crush on Seongwook for a long time, it has nothing to do with these pranks, she had that and she probably still has it, they all 3 know about that. So, as you can figure it out, Subin was happy there to learn they were "finally" together and the reason why she didn't like it was a prank, she left and told them to be together.