It might be dishonesty, but it might be incompetence instead. Consider starting with a letter pointing out the discrepancy and saying that you hesitate to pay when there is so much uncertainty about what your obligations are. If you allege dishonesty and it turns out to be either incompetence on their part or a misunderstanding on yours, then accusing them of dishonesty will hurt your credibility. If your letter either goes to the boss or works its way to the boss, then he or she will know whether the company's employee is trying to pull a fast one. Let them draw that conclusion on their own.