Cooper’s reaction indicates that it did not come from the CIA, and the only other agency there was the FBI. Since it was not likely to be Frank, Sarah, Victoria, etc., it points to the FBI.
The problem of course is that just because Cooper called for hold-fire, does not mean that someone else from the CIA couldn’t have done it. As you suggested, it could have been another CIA agent working under direct orders from the higher-ups, working for his own agenda, or even just a case of nerves.
Also, Dunning probably has some more guards and could have tripped some sort of alarm to send for reinforcements.
Everything about that scene (especially the slow-motion and muted sound) make it clear that the shot is supposed to be dramatic and mysterious, so we are not really meant to know for sure. Plus, don’t forget that the scene leads immediately to an action escape, so the viewer is probably not meant to dwell on the facts and that scene served as a sort of transition to
their unlikely escape.