It's your responsibility, not the SEP-IRA custodian's responsibility, to track the year for which a SEP contribution is made. However, only an amount contributed in 2018 (or in 2019 before the due date of your tax return) can be treated as contributed for 2018 rather than for 2017. If you keep these contributions made in 2017 in the account by not having the nondeductible portion returned, you'll have to file Form 5330 and pay a 10% excise tax on the portion not deductible on your 2017 tax return. After doing so, you can then treat the excess contributed in 2017 as a deductible SEP contribution for 2018. Better would be to obtain a return of contribution, if the custodian allows this for SEP contributions.
TurboTax does not support Form 5330.
Two possible alternatives, though: First, if you had income from self-employment in 2016, did not already contribute the maximum for 2016 and some of the SEP contributions made in 2017 were made by April 18, 2017, you might be able to amend your 2016 tax return to treat some portion of those as SEP contributions for 2016. Second, if your SEP-IRA custodian permits regular IRA contributions to the SEP-IRA account, you might be able to get the custodian to treat a portion of your contributions as regular traditional IRA contributions in their reporting on the 2017 Form 5498 from this account. A regular traditional IRA contribution may or may not be deductible, depending on your modified AGI for the purpose.
