It confuses a lot of people. Code W means employer-based contributions, either for you or by you. They need to be lumped together, as there is a yearly limitation on how much can be contributed to a person's HSA period. It is presumed that the employer already accounted for your own payroll contributions by removing them from your wages, but the W is only there to show how much was contributed to your HSA by you or for you.

See W2 instructions and the description of Code W:

W—Employer contributions (including amounts the employee elected to contribute using a section 125 (cafeteria) plan) to your health savings account. Report on Form 8889, Health Savings Accounts (HSAs).

In order for HSA contributions to remain without any tax consequences, Form 8889 must be completed on your tax return. On Form 8889, you describe your coverage in a High Deductible Health Plan, including who is covered and when. HSA contributions are not pretax or without tax consequences until Form 8889 says they are.

When you add the W2 and put in Code W, you have not yet completed Form 8889. So, Turbo Tax puts the excess contribution penalty on those contributions "up-front". Turbo Tax takes it off as soon as Form 8889 is completed.

You complete the screens for Form 8889 by going to:

Federal Taxes- Deductions and Credits- Medical- HSA

Assuming you had a HDHP for the year, and the amounts that went into your HSA were within the limits, your return would go back to where it was before you put the W in.