What do I do if a Clerk Magistrate is not following procedure?

Clerk-magistrate is not a term used in any court with which I am familiar. In any case you do not provide enough information for me to provide a useful answer. Perhaps you could write the clerk or magistrate, setting forth the basis of your belief that a false document was filed.

Most clerks are supervised by a presiding judge. I would explain the facts to the judge in a formal written communication.