It's not an error. You took a direct flight, which is a flight that has at least two segments (so it stops at least once), but the same flight number for all segments. Mileage credit for direct flights is calculated and credited to you as if you took a nonstop flight.

Maybe someone else can weigh in on why it works this way. I've never understood it, but I definitely try to avoid those flights because of the mileage implication.