So here is my story... Or more accurately, my father's story.

We have been going along just fine, my mother has always filed the tax return for her and my father. Never an issue in 50 years of marriage. Suddenly, a letter is received from the IRS saying the withholding that we reported on their taxes for 2014 is incorrect. That letter is ignored, not on purpose, but for other reasons. Another letter is sent, and as you know, they only get more severe. Here we are, it is 2016 and the final letter arrives. The one stating a lien is forthcoming unless payment is made. This is where my father and I become aware of the situation. My mother had a brain tumor and had stuck the previous letters away and forgot to mention to anyone. We only found out after she passed away and the final letter came.

In a frenzy, we pay the money before we even have a chance to look at the reasoning. Close to $5000. (That's a lot for us). After all is said any done, we investigate closer and realize that my father's employer gave him a W2, but it never went any further than that. Only the income was reported to the IRS but no withholding apparently (Even though our version of the W2 shows withholding and it was taken out each paycheck). I came to this conclusion because the exact amount of tax that was owed is the same as the withholding on his paycheck.

Next thing you know, another letter arrives. Guess what? The same things is being said about 2015. This time, however, we receive the first letter and nip it in the bud by sending in our copy of the W2. After months of waiting, we receive a letter saying we no longer owe anything from 2015 because of our proof.

As you can guess, the payroll clerk at my father's employer is no longer employed there and is facing criminal charges.

Now, sorry for the long story, but I felt it was best to know the circumstances.

My question is:
We know we did not actually owe the IRS the money we paid for 2014. How do I recoup that money? Do I file an amended return? Do I contact the IRS and say, "Hey, this is what happened"? Any light someone could shed on the subject would be extremely helpful.