It is considered a good thing to hurt the muscles. Muscles are not afraid of pain. In the Practical Method system, we do not train the muscles. Train muscles means to bulk up the muscles to make them strong. We elongate muscles. This requires a different method of training.
It is a bad thing to hurt ligaments and bones. Ligaments and bones are afraid of being shortened, not elongated. Postures should be large and low so as to allow the elongation of ligaments and the skeletal structure.