Ah, so you also had a mix of withholding and estimated payments. Making estimated payments unevenly throughout the year can make it appear that you owe a penalty. If you want to get rid of the $4 penalty for 2023, you would fill out Form 2210 Schedule AI. I assure you it is a pain and most people would consider the amount of time they'd spend on that form to be worth way more than the $4 they'd save. Personally, if it were me, I would just check the box in TTax that says something like "let the IRS figure my penalty". I would not file Form 2210. Odds are in your favor that they wouldn't penalize you at all. Even if they do send you a bill, it's not going to be more than the penalty that would have been due on the date you actually pay the tax due. The $4 is going up a bit every day that you wait to pay, so by April 15th, it might actually be $5 or $6.
For 2024 -- the refund you're getting for 2023 is not related to the quarterly payments you owe for 2024. I think TTax is taking your total tax liability from line 24 of your 1040, which must be about $1297 x 4 = $5188 and using that to determine the quarterly payments for this year. Ideally you would increase your withholding from your annuity and IRA withdrawals to cover the entire tax and not make any quarterly payments. If you can't or don't want to do that, then the other way to do it is to subtract the expected withholding from your 2023 tax liability and divide the remainder by 4 and use that for the quarterly payment amount.
Yes, you should make a quarterly payment in Dec, even if you have withholding in that month. If you choose to do estimated payments, make all 4 payments.