I made a mistake in using Turbotax where I added my self-employed consulting income twice. This resulted in greater taxes, but also an excess SEP IRA contribution. I am working on the 2015 1040X. Do I need to fill out a 5329 or 5330 for 2015? I am hoping I can do the 1040X with the corrected income and file with the correct SEP IRA contribution. I hope to then decrease my 2016 SEP IRA contribution. Does this sound correct?
Since your SEP contribution was made in March 2016, you can allocate the portion that was not a deductible contribution for 2015 as a contribution for 2016 instead. The SEP-IRA custodian only tracks and reports the year in which a contribution is made, not for which the contribution is made. It's your responsibility to track the year for which contributions are made. If your 2016 self-employment profit is sufficient, you should end up with no nondeductible contribution that would need to be reported on Form 5330.