OK. We need to establish if the $3,000 is showing up on your tax forms, specifically on line 8f of Schedule 1 (1040). If it does not appear on Schedule 1, then you are OK.
There are various screens like Income summary and Deduction summary that are not real tax forms. If this is the case, because the distribution on the 1099-SA is potentially taxable, they put it on the Income summary (not tax form) and didn't remove it when you entered the fact that the distribution was all for qualified medical expenses.
So long as your actual tax forms are correct, you are good to go.
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