Originally Posted by jsloan

It’s not an error at all. It’s just not computing the price the way you’re suggesting.

In most cases, when changing the return leg of an itinerary, the entire ticket is repriced as if you’d bought it that way originally. Thus, you’re effectively exchanging a partially-used ticket that cost $X for a partially-used ticket that would have cost $Y; it’ll show you ($Y-$X) as the “fare difference” and it will tell you that it’s applying $X toward the total ticket purchase.

It’s a bit confusing, but it works out in the end.