Three weeks is long enough that this needs to be addressed formally rather than through casual inquiries that go nowhere.
Your son needs to request an appointment with his counselor and present the facts clearly and respectfully. That means having the specifics ready: the date the order was placed, what was ordered, what was received incorrectly, and the exact amount owed in credit. The more organized and factual he is going in, the harder it is for the issue to get dismissed or delayed further.
The counselor has the ability to look into commissary account discrepancies and escalate to the appropriate department if needed. Commissary operations are typically run by a separate department within the facility, and the counselor serves as the bridge between the inmate and that administrative function.
If the appointment with the counselor does not produce results within a reasonable timeframe, the next step is a formal written grievance. The grievance process creates an official record that the issue was raised and requires a documented response from the facility. That paper trail matters, particularly when money is involved.
From your end, encourage him to stay calm and respectful throughout the process. Inmates who come across as aggressive or demanding tend to get slower results than those who present their case clearly and let the facts speak for themselves. The $13 credit and the missing items are legitimate issues the facility is obligated to resolve, and a well-documented, respectful approach is the fastest path to getting both handled.