What the brokerage did and reported is fine. The brokerage adjusted your contributions to be the permissible SEP contribution plus a regular traditional IRA contribution, then made a return of the regular traditional IRA contribution. The result is that there is no excess SEP contribution. You'll receive a 2022 Form 1099-R with code P (and code 1 if you are under age 59½), indicating the taxable earnings that are required to be included on your 2021 tax return. You might as well wait until this form is provided to you in early 2023 before amending your 2021 tax return to include these taxable earnings.
As I said before, the result is that the amount in box 1 of the Form 5498 is from your compensation, so that either came from your net profit or was required to be included on your W-2, depending on the type of business entity.
Note that a SEP IRA account is permitted to receive regular traditional IRA contributions as was the result of the brokerage's adjustment. That was followed by a return of that regular traditional IRA contribution, adjusted for gains, with the result being as if the regular contribution was never made. No regular IRA contribution gets reported on your 2021 tax return, only the taxable gains must be reported on your 2021 tax return. The gains are subject to ordinary income tax and, if you were under age 59½ at the time of the return of contribution, to a 10% early-distribution penalty.
