It is possible to do a same-day roundtrip between EWR and MSY for just over $300 by pasting together multiple fares. C.O.O.L. will fare this out properly the first time, but if you save the itinerary and try to ticket later, it will re-fare at around $2000. The only solution is to cancel the reservation, start over, and ticket immediately. (I ought to know, as I did all of this last month.)
If it makes you feel any better, NWA.com does exactly the same thing.
Obviously, the fault lies with the underlying Expedia-based software, and not with the airlines.