Overpaid NYS Taxes, Refunded, Then Charged Again Later

Hi everyone,

I'm a 1099 employee and pay estimated taxes quarterly. I filed my taxes on 2/26 and received a refund check in the mail on 3/4 since I overpaid for the year.

On 4/15, the amount I owed for the 2025 was deducted from my account again (meaning I paid double the amount I actually owed). I know for a fact this is a computer error and I was hoping the system would catch this and automatically send me another refund check but it's been 2 1/2 weeks and I'm not sure if I should continue to wait or reach out (or frankly who I should even reach out to).

I checked my refund status and it says I don't have anything pending. I know a lot of people have had issues and I realize waiting isn't uncommon – I'm just looking for guidance since I've never had to deal with this before.