Perhaps, but if that was the case, then this would impact thousands of people each week. There would be widespread confusion and discontent among riders and the glitch would have been fixed pronto.

That said, the easy way to avoid this is to book your next trip as two separate one-ways. Except for when using a B1G1 coupon, there is no financial incentive on Amtrak to book a round-trip ticket as opposed to two one-ways.