That happened to my group a lot today. Turns out the noob we let in with us was shooting Crota with his primary while he was kneeling to "try and keep his shield down between dropping him." Once we convinced him that we'd boot him if he didn't stop, it never happened again. Once it was clear you stop shooting when he kneels, we had one person (me) call out when to fire rockets again after each kneel. Worked perfectly and we were able to get him kneeling 3x per sword.