Since the SEP contribution was made after the extended due date of your 2018 tax return it constitutes a SEP contribution for 2019, not for 2018. You are not permitted to report this on your 2018 tax return as a SEP contribution.
If this contribution made for 2019 is in excess of the amount that you will be permitted to contribute for 2019, you must obtain a return of excess contribution of the excess amount. You must report the net amount on your 2019 as a SEP IRA contribution. If you have an excess SEP contribution do not obtain a return of the excess contribution you must file Form 5330 and pay a 10% excess contribution penalty. TurboTax does not support Form 5330.
A SEP-IRA custodian only tracks and reports on Form 5498 the year in which a SEP contribution is made, not the year for which the contribution is made, so Vanguard did not "accept this as a 2018 employer contribution," they only accepted it as a SEP-IRA contribution It's the responsibility of the employer, not the SEP-IRA custodian, to do that tracking and reporting on the employer's tax return.
