They played an active role and escalated the situation by throwing stones. This crosses the ethical boundary. Agents can be allowed to be offenders, or else they create the situations they shall investigate. This won't play well at court, and in public opinion. You can't reasonably blame protestors for violence if actually agent provocateurs take part in that, possibly even trigger it.
Palestinian Red Crescent say 23 injured around West Bank and Jerusalem (Haaretz)