You should file a corrected 2019 Form 5329 along with Form 1040-X primarily to correct the $12 of excess that otherwise carries forward to line 18 your 2020 Form 5329. With this amendment you can also claim a refund of the $1 penalty paid unnecessarily. (On the Form 1040-X you can choose to credit the $1 refund toward your 2020 tax liability).
Line 10 of Form 1040-X, Other taxes, will show a change of negative $1 due to eliminating the $1 penalty on Part IV of the amended 2019 Form 5329. In the explanation that you provide with the Form 1040-X you will indicate that the correction is due to having previously reported on Part IV of Form 5329 a $12 excess Roth IRA contribution that was not actually made.