There is really nothing to explain. The reason that the employer paid you some amount above your regular wages (a fringe benefit, supplemental wages) and included it in the total wages shown on your W-2 is irrelevant. The employer simply paid you some total amount of reportable wages and you yourself paid some amount of points, two independent entries on your tax return. The tax code requires that your wages be included in income and a separate section of the tax code allows a deduction for points paid. The two are unrelated.
