If your employer is not reporting their contributions to your HSA and you live in either New Jersey or California, it is a serious problem, because those states do not allow HSA contributions so TurboTax adds back the code W amount (which you now realize is wrong).
For everyone else, you can correct the situation as described above: on the screen where you are asked, "Did your employer tell you about any other HSA contributions?", you can answer "yes", and then enter the amount on the line which states, "employer contributions that were not reported on your W-2".
This will cause TurboTax to correctly complete the form 8889.
Then have your employer read the instructions for code W in the Instructions for the W-2 on page 20:
"Code W—Employer contributions to a health savings account (HSA). Show any employer contributions (including amounts the employee elected to contribute using a section 125 (cafeteria) plan) to an HSA. See Health savings account (HSA)." The IRS instructions could not be more clear.
