Been there, done that... Something like this happens at least a few times a year, so I am not sure why this made the news. it usually happens because of human error overriding the many protections that software have to prevent it from happening.
To make matters worse, the tickets are usually sold in mater of minutes because the algorithms that calculate the most efficient route from point A to point B lock on to the fare and use it for everything.
From someone on the inside, I've heard that they (well, the "line workers", at least, as opposed to Management) have been going through hell since launching the integration of their systems with... Continental's, IIRC (so many mergers; I'm forgetting which involve who). Apparently, they've escalated from SNAFU to FUBAR.