SEP contributions are employer contributions. The employer deducts the contribution on your employer's tax return. You do not deduct it on your individual tax return .
Did you make a regular personal IRA contribution independent of the SEP contribution? (Normally one does not make regular personal contributions to the same SEP-IRA to which employers make SEP contributions. Some SEP-IRA custodians don't allow it and even if they do, special care must be taken so that the custodian records it as a regular personal IRA contribution and not a SEP contribution.)
