Penalty for estimated payments underpayment. I understand that if the total tax due is under $1,000, (it is,) there is no penalty. Turbo Tax says I own $9 in penalty.

That's "total tax", not "amount you owe" or even "refund"

You might be able to eliminate it or at least reduce it. You can go to Federal Taxes tab or Personal tab, under Other Tax Situations and select Start by the Underpayment Penalties. You will answer a series of questions that may reduce or eliminate the penalty. Or you can elect to have the IRS figure the penalty for you. It's form 2210.

It's under

Federal or Personal (for Home & Business Desktop)

Other Tax Situations

Additional Tax Payments

Underpayment Penalties - Click the Start or update button

I had a refund once and still had a penalty for not paying in evenly during the year.