this has happened to me twice on expedia in the past month. both times I was quoted one fare AND fare basis but the issued ticket was charged at a different fare and fare basis. When I called Expedia they gave me the same line about my complaint being the first. So I did exactly what CO FF has said. After receiving the dispute from my CC company they quickly reversed their stance and credited back the difference. So if the the fare differences are large enough you should pursue this through your CC company.