It’s likely that the underpayment penalty that you saw was an estimate and Form 2210 wasn't required with your return. The IRS doesn’t require it’s filing unless you are requesting a wavier, you’re annualizing, you’re treating your withholdings as paid when actually withheld, or your filing state changed from or to Married Filing Jointly between the tax years. Check your tax records to confirm.
The IRS will figure out the penalty for you and send a bill, or in your case, where there's an overpayment, they will refund it. You can read more about who has to pay the penalty and the various exceptions here. The IRS notice should explain why they changed the penalty amount, and what to do if you disagree.
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