A $360 penalty corresponds to an excess contribution of $6,000, not $5,500.
The penalty will be present until you have entered your W-2(s) with box 1 amounts (reduced by any amount in box 11) totaling at least the amount of your Roth IRA contribution. The contribution will also be an excess contribution if your modified AGI for the purpose exceeds the limit corresponding to your filing status. To see if the excess contribution penalty is actually still present, check Schedule 2 line 6 after making all of the entries.
Also be aware the any earnings excluded under the Foreign Earned Income Exclusion (if any) are not earnings that will support an IRA contribution.
