The penalty is based on what did not get paid for the period's due date: "The penalty is figured separately for each installment due date. Therefore, you may owe the penalty for an earlier due date even if you paid enough tax later to make up the underpayment. This is true even if you’re due a refund when you file your tax return."

Read this:

https://www.irs.gov/instructions/i2210#idm140641543271280