I am helping a married friend with her taxes. She is married to a man who is on SSA disability for a head injury. He receives less than $15,000 per year and has never filed taxes while single due to it being only the SSA. She works as a therapist and makes ~$45,000 per year. Now that they are married, it is my understanding that whether they file married filing jointly or married filing separately they have to include his SSA (at least a portion as determined by the form that assists with the calculation of this) He also has an investment related to the head injury law suit settlement that has an interest gain of $1000...

My question is if this is indeed the correct way for them to file. She seems to think that if he never had to pay taxes on that money before... why does he now that they are married? Can she file taxes as Married filing Separately and pretend that SSA money doesn't exist? And then he doesn't have to file at all? I can admit the logic seems a bit twisted... that as a single man he didn't have to pay and now as married it counts?

You can only file as Married Filing Jointly or Married Filing Separately.
Social security disability benefits may be are taxable only if the total the total income exceeds the base amount.

The base amount for Single is about $25,000 so if he did not pay any taxes in past it is fine.
For Married Filing Jointly, the base amount is about $33,000. So your friend should file as Married Filing Separately and her spouse does not have to file taxes if his only income is SSA disability.

I guess I am confused... we spoke to the IRS who led us to believe that because they are married that they have to pay on a portion of his SSA... based on a formula provided in the 1040... now that she has filed 2 years to her disadvantage... what do we do now?

So you are saying that she simply files on her income alone as Married Filing Separately and ignores all of his SSA income?