Did your payment with Extension show up on schedule 3 line 10 and goes to 1040 line 31? Did Turbo Tax calculate any penalty on 1040 line 38? Turbo Tax only calculates an estimated penalty amount. Even if Turbo Tax entered a penalty on line 38, it's common and normal and expected for the IRS or state to bill you for more or send you a refund. They don't know for sure when the IRS will get your tax due payment.
