It's your responsibility, not the IRA custodian's responsibility, to record the year for which the SEP contribution is made. The custodian is only responsible for recording the year in which a SEP contribution is made, not the year for which a SEP contribution is made. The designation of the year to which the contribution applies is made by the amount that you report as the self-employed retirement deduction for that year.
There is nothing for Fidelity to do. Whatever amount was deposited in 2024 must appear on your 2024 Form 5498 regardless of the year for which the contribution was made (in this case part for 2023 and part for 2024).
