I included both the 1099-R for the 401k and the 1099-R for the distribution that puts me below the threshold.
You need to have a code "8" in your Form 1099-R box 7 for the refund of your excess contributions. That way they will be applied to 2024 as opposed to 2023, which would happen if you had a code "P".
@ThomasM125 would you know if something else might be explain the alert from TurboTax?
These are the instructions you will see in TurboTax when you are notified that you have an excess contribution. They assume the correcting distribution was received in 2025, but you can try the entry even if you received it in 2024 as it won't adversely affect anything. You can also try deleting your W-2 entry and Form 1099-R entry and re-entering them as sometimes things will calculate better when you do that.