It's not clear whether the payments you are talking about were applied to 2018 or 2019. If they were applied to 2018, the IRS probably will send you an additional refund for the extra payments, but it might take a while. If you don't get a refund in a couple of months, call again and ask them to send you a refund of the excess payments.
If the payments were applied to 2019, the money is just going to sit there until you file your 2019 tax return. Be sure to include it in the payments when you prepare your 2019 tax return. That's how you'll get the money back.
