I now have a script for the phone call with these:
Me: "Could you look up the cost for this trip in the system?"
Phone Agent: "Yes Mr. DCAHome, the base fare for this trip was $500."
Me: "Thanks. Could you look up the credit I received for my MQDs?"
Phone Agent: "Yes. It looks like you received 350. That looks like a problem."
Me: "I agree. Would you be able to fix that?"
Phone Agent: "I'll have it re-queued so they can manually re-calculate the credit."

I make this sound like a joke, but when I've started out by saying the MQDs were incorrect, I've had phone agents try to convince me that MQDs aren't always equal to the base fare. HUCA.