HSA Excess contributions

You have to complete the entire HSA interview to certify that you have qualifying HDHP coverage.  Until you complete that certification, the HSA contributions will be added back to your taxable income.  Run the HSA interview on the Deductions page or run the 1099-SSA interview on the income page. 

It is more likely that you did not tell TurboTax that you had the proper HDHP coverage in the HSA interview. Another possibility, less likely, is that you accidently indicated that you were a dependent of another taxpayer (dependents cannot contribute to an HSA).

Go back into the HSA interview and make sure that you showed HDHP coverage for the year.