We don't know for sure what the clerk said-- all we have is something from Berg's paralegal, and I personally think that Berg's credibility is questionable. But it does happen sometimes that clerks make mistakes, and there is a procedure for asking the judge to correct them 9which Berg didn't follow).
But all of that is a sideshow here. The judge's order has nothing to do with whether Berg followed (or disn't follow) the clerk's alleged advice. Berg is being called on the carpet for missing three deadlines to respond to the motion to dismiss. Instead of responding, he filed something about how the clerk supposedly bullied his paralegal-- not a response to the motion to dismiss.
True, this is a tangential issue...however, if that is indeed true that the court required something that isn't required...that's hardly a sideshow IMO.
It could be seen as judicial activism or the judiciary acting as lawmakers.
That would be another major Constitutional issue there unto itself.