In The Great Game, Molly hasn’t yet grasped the idea that this could be something permanent, the little man following Sherlock around. She doesn’t even bother to remember his name! Three episodes later, and she has come to terms with the fact that Sherlock will probably never love her back and yet she is not jealous or doesn’t have a grudge against John. She sees Sherlock is hurting and the only reason she knows this is because she has learned he only shows his pain when John is not looking.