You are correct, you are not allowed to claim Earned Income Credit, if you are married filing separately and live with your spouse. TurboTax completes your return based on the answers to the questions. You might have answered something incorrectly, your filing status should be Married Filing Separately. You should go back through your information and check to see if any questions were answered incorrectly. To do this:
- Open or continue your return in TurboTax.
- Select My Info in the menu.
- Next to your Filing Status click Edit and go through all the questions and make sure you answered correctly.