A stipend is a fixed sum of money paid periodically for services or to defray expenses. The fact that remuneration is termed a "fee" or "stipend" rather than salary or wages is immaterial they are subject to employment taxes. Payment of stipends is made according to the policies of the governing entity.
Since the stipend is not considered to be a part of your base yearly salary or hourly wage, unless the stipend amount was guaranteed to you, either by contract or labor agreement, you have no recourse against your employer.