Did you do the HSA interview (Deductions & Credits->Medical->1099-SA, HSA, MSA)? Did you go all the way through it, until you see HSA Summary?
It sounds like you enter your W-2 with a code W amount in box 12, but never did the HSA interview, so TurboTax assumes that you didn't have any of the required HDHP coverage. Hence all contributions are in excess.
Please follow the navigation above (in bold) and do the HSA interview.
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