This requires filing a 2018 Form 5330 and must be filed separately. The excess contribution is reported on Schedule A of Form 5330. At this late date, I think there is a late filing penalty (in this case, it appears that there is a $60 late-filing penalty in addition to the $60 excess contribution penalty on the $601 nondeductible (excess) SEP contribution), but let the IRS bill for any late-filing penalty.
