There is currently no penalty or requirement to payback any stimulus payments received. The IRS has not not issued any guidance for those individuals who indicated on their already filed return that they did not receive a round two payment and it then showed up.
Due to the timing of the second round payments and tax filing season this situation is very common.
The Recovery Rebate Credit is based on the information in your 2020 return. The total credit you are eligible for is added to your tax return based on the following calculations:
Round one: $1200 (2400 filed jointly) plus $500 for each dependent age 16 or under
Round two: $600 (1200 filed jointly) plus $600 for each dependent age 16 or under
That total credit you are eligible for in 2020 is then reduced by any stimulus amounts you received in rounds one and/or two. The remainder is on line 30 of your form 1040 as a refundable Recovery Rebate Credit.
Here is a link with more information on the Recovery Rebate Credit.