You are not paying tax on them and they are not deducted from your refund. Turbo Tax started out by assuming you didn't get it and giving you credit for the whole amount so your refund was too high to begin with. Then when you entered what you already got the starting refund was reduced or the tax due increased. Otherwise you would be getting the Stimulus amount again on your tax return.
Look at your return. The Stimulus payments do not show up anywhere as taxable income so you are not being taxed on it. And they are not being subtracted anywhere on your return either.
