Sorry to hear of your loss and your trouble in using electronic filing.
Your mother's filing status is single since your father was not alive in 2012.
Unfortunately when the e-file error message is that the SSN was on another return there is nothing that you can do in the return you want to electronically file that will get past that error message.
Presuming that there is not any error in the number being used for her you can not e-file when the IRS system indicates that number has been used, sorry.
You did not file another return but the IRS system is detecting her number as having been used already so it simply will not allow a second return with the same number to be filed.
Your only recourse is to print out, sign and file the return via the postal service. When more than one return is filed with the same SSN the IRS has to investigate prior to processing so this situation (even if it was simply a mistake by someone else typing in the wrong number) will often result in a delay in processing the return.
Please ask if you need clarification.
How do I sign the tax return since my Mother is deceased? I am the executor of the estate, should I include the death certificate and Letters Testamentary with the return?