If married filing separately, I can't think of a reason for the program to ask this question at all. For that reason, I suspect that you are using the same online account you used in the past for a joint return, and changed to MFS, but the program still contains tax file data and worksheets in the name of your ex. It can be difficult to change filing status with TT online because most of the important worksheets are hidden and not directly editable. You may want to quit, make a new account, and start over fresh, so there is no leftover information about your spouse.
