Your experience is actually a common complaint. Southwest has never been known for particularly robust IT systems, and sometimes there is a disconnect between the fare database and what is displayed online. Also, fares do change frequently, and out-of-sync seat availability updates at a given fare level cause fares to be displayed that are actually no longer available. You were fortunate that the phone rep was able to see the lower fare and book it for you -- often when this happens that's not the case.
