So I think I figured out the problem. In the HSA interview, there is a question about Archer MSA contributions but it incorrectly asks for the total Archer MSA and non-Archer HSA contributions. Then TT adds that number to HSA contribution it already has from the W-2, and which of course results in TT concluding that there was an excess contribution. I removed the number in my answer to the Archer MSA question (despite the text explicitly asking for total contribution including to Archer MSA and non-Archer HSAs), and that fixed the problem.
