So, if the ML Coaches had their conference, and got the referee to agree that he misapplied the rules, the result was changing a ruling of "no call" to a ruling of "Unnecessary Roughness" or "Unsportsmanlike Conduct (UC)". Either of those violations carry the same penalty, and both are not the same as Flagrant Misconduct. Thus, the ML Coaches either settled for the UR or UC, or the referee's award of only a UR or UC would have resulted in a Coach Misconduct on the ML Coach for questioning the judgment of the referee.
Was the ML coach given a Coach Misconduct? If not, then I don't see why the ML Coaches would protest the match. It would mean they got the ruling they believed was the correct rule application, and then wrestling resumed.