No, the 10% early withdrawal penalty will only apply if you are under age 59½. Since you are over 591/2 please make sure you enter the $3,000 on the "Did you use your IRA to pay for any of these expenses?" screen under "Another Reason" to get the exemption from the penalty since you are over 59 1/2. You will get to the screen by continuing through the questions after you entered your 1099-R.
If you do not remove the excess contribution then you would have to pay a 6% penalty each year as long as the excess is left in the account.
Please see What happens if I made an excess Roth IRA contribution for additional information.
[Edited 1/27/2022 | 10:01am PST]
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