She had a crush on him, but she was too afraid to just tell him and when Lisa believed Mihouse liked her, she was wrong when she found him with that woman. Milhouse was getting sick of Lisa's "teasing" .
I can understand him, sometimes she's a bit selfish. In some of the newest episodes, it was shown that Lisa seems to like Milhouse more than a friend, and she even accepted to date him on 'Moonshine river'. But even now she plays hard to get, as she denied it wasn't a real date.