I think that the W-2 needs to be entered as is and you probably need to trick TurboTax into treating Spouse's contribution as being deductible instead of being treated as an employer contribution. I think I get an appropriate result by, during Spouse's HSA questions, indicating that the $3,000 was a personal contribution, that your employer told you about other contributions and that $3,000 was a contribution for the prior year. Indicating that it was for the prior year just removes it from line 9 of Spouse's Form 8889.
