TurboTax's behavior is correct and the CPAs and other tax software providing a different answer are incorrect.
Unless the SEP plan is a SARSEP established before 1997, all SEP contributions are employer contributions. Only employee contributions to a workplace plan, not employer contributions, are qualifying contributions for the Retirement Savings Contributions Credit. See IRS Pub 590-A Chapter 3 for details.
Note that although it is not recommended to mix SEP contributions and regular contributions to a SEP-IRA, it is permissible to make a regular contribution to a SEP-IRA as long as you make it clear to the IRS custodian that the contribution is a regular contribution and not a SEP contribution. (Making regular contributions to a separate ordinary IRA account completely avoids the potential error of the contribution being reported incorrectly on Form 5498.) TurboTax's message that contributions to a SEP-IRA qualify for the credit only applies to regular contributions made to the SEP-IRA and salary reduction contributions made to a SARSEP.
If you qualify for a regular deductible traditional IRA contribution, you would do best to allocate your deductible contributions first as regular traditional IRA contributions and only after you've made the maximum permissible regular IRA contributions allocate any additional amounts as SEP contributions.
