If you didn't file for an extension already, the due date of your return was April 15. If you didn't withdraw the excess prior to that due date you can't remove the penalty for 2024. You don't need to file an amended return. You should receive a 1099-R with a code P for the excess withdrawal to report on you 2025 return that will stop the penalties.
Code P: Taxable in prior year. This code applies to the portion of the distribution that consists of the initial excess contribution. It signifies that the excess amount is taxable in the year the contribution was originally made.
Code 8: Taxable in current year. The earnings on the excess contribution are reported on a separate Form 1099-R with code 8. These earnings are taxable in the year they were distributed to you
Hope this helps!
Cindy
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