The deadline for a SEP contribution based on 2018 self-employment earnings is October 15, 2019 only if you requested a filing extension. If you did not request a filing extension, the deadline to make a SEP contribution was April 15, 2019 and it's possible that your $549 SEP contribution is an excess contribution unless you treat it as a SEP contribution for 2019, assuming that you have self-employment net earnings for 2019 to support the SEP contribution for 2019.
Since you had sufficient compensation to support the regular personal traditional IRA contribution, the regular personal contribution that you made was not an excess contribution and there was no requirement to have that contribution returned. If you did not participate in any retirement plan of some other employer for 2018, your personal contribution was deductible (long as you made no actual SEP contributions). If you did participate in another employer's plan, your AGI made your your regular personal traditional IRA contribution nondeductible but not an excess contribution.
Regardless, yes, you'll need to report the 2019 Form 1099-R based on the code in box 7 as I described earlier.
