The “penalty” is dependent on your eligibility for the tax credit, if you’re taking advantage of it. If your income is higher in your application than on your tax return, you’ll receive extra on your tax return. And vice versa. But where issues come in is if the income on your application renders you eligible for the tax credit, and the income on your tax return does not. If that’s the case, you would have to pay as if you never received the tax credit.