Kraco said: A better question is why Shirou is wearing shoes indoors.
If I were to think an scenario for this, then she'd probably decided to do this to convince Shirou to make him to choose her. And because of her nerves and tsunderism, probably as soon as she heard that Shirou arrived home, she just ran to him and drag him inside (without giving him time to remove his shoes) and immediately removed her skirt.