Yes, if she was able to make Roth IRA contributions for 2024 then you can apply the excess to 2024 and avoid the 6% penalty for 2024.
If she made already Roth IRA contributions for 2024 she could still apply the 2023 excess to 2024 and then remove the contribution for 2024 as an excess contribution plus earnings before the due date. Since she made the contribution for 2024 in 2025 she most likely would get a 2025 Form 1099-R with codes 8 and J and this would be reported on the 2025 return.
Yes, the 2025 Form 1099-R for the 2023 excess will have to be entered on our 2025 return.
I would consider to enter a substitute Form 1099-R with code J if they refuse to correct the form. Then you can add a statement explaining that this was a 2023 excess contribution removed after the due date and Fidelity is refusing to use the correct code. In the follow-up Roth questions after you entered all 1099-Rs you will include the 2023 excess in the net contribution amount. You can withdraw contributions you made to a Roth IRA anytime, tax- and penalty-free.
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