The Anime studio never really explained the logic behind that. Presumably, Muramasa's "materialisation" ability was not sealed for one reason or another. Perhaps because at the time, Muramasa and Koga were completely out of sync, to the point that Koga could no longer call Muramasa out - because Muramasa couldn't hear Koga's voice. But really, we can only guess at why the seal only sealed Koga.