Wait, does your return line 37 tax due show just the $89 you still owe or the total 89+ extension payment? It should be only the $89. Make sure you are getting credit for the extension payment on 1040 line 31 which comes from schedule 3 line 10. If it's not there you need to enter it.
By the way, any penalty on line 38? You can probably eliminate that. Is the penalty $89? If Turbo Tax thinks you didn't pay the extension payment it may give you a penalty.
