I didn't overfund my HSA but I'm flagged for potential excess contributions. Called up HSA and they don't see any excess contributions or withdrawls. Why update 8889-T?

I'm asked to check the 8889-T box 12 for amount that was withdrawn due to over funding my HSA. I didn't and confirmed with HSA. Do I put 0 for amount withdrawn or what's in box 12 of W2?

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the most common reason for this issue is if the HSA was funded through payroll deductions and then you entered those deductions again as personal contributions. payroll contributions are only reported on line 9 of the form and come from item 12W on the W-2s.