I don't think the lack of coach thru space is actually a 'glitch', but rather a result of how space is programmed into the reservation system, where they control how many 'seats' are available between each city pair. It is an ancient program that may have been designed with good intentions, as to make sure that each market may have some availability, up to a point, when Space and Equipment control may manually make adjustments according to demand, and maximize yield management. Good agents knowing this, as gn2276 mentioned, learned how to 'work around' this, and piece together with two or more segments, and then manually price the ticket to the thru fare. Usually it was the other way around...they would block local segments, such as DEN to GSC, to preserve thru space for longer trips...
Back when I sold tickets at Denver, I would use the three trains (CZ, Pioneer, and Desert Winds separate inventories to piece together space for passengers to work around "sold out trains". More often than not, I could get passengers where they were going that way...something that Arrow should have been programmed to automatically do by itself, IMHO.
Another trick I employed to take care of my customer's, was when the 'discount' thru seats were no longer available, I would check to see if I could piece together segment discount seats, using the same or the other train's inventories to do so, and again, if successful, would manually price them to the thru discount fare. Back then, there were only two "buckets" of inventory...regular "C" seats, or discount "CA" seats.
Taking care of customer's was good for the Company in the long run, and for station agent job preservation as well, as customer's could also choose to buy from travel agents, or from the Reservation Sales Offices. Not likely the latter two would go to the trouble that we would for a customer coming down to the station to make the purchase personally.