After you file

Hi there! Thank you for your response. 2019 was a horrible year so we did not file our taxes for 2018 until January 2019.

Because they were late, I was able to prepare the return through TT but was not able to file through TT. I had to mail in a paper copy. We even received a refund.
Waiting and waiting for our stimulus to arrive, I called the IRS and 3 or 4 people later, found out that the box "someone can claim your spouse as a dependent" was checked.
This box was not checked on our return, but the IRS claims the box is checked. I have been around and around, I even went to the IRS office and was told I needed to do the work and pay $50 to receive a copy of the return they received so that I could prove the error was made on their end.
Instead of waiting for 2020 tax season, we trying to amend the return (which was also suggested by the local IRS office) It doesn't seem that the 1040x is addressing our specific situation, and is why we are reaching out. 
What is shown on the copy of the return the local IRS printed out for me is EXEMPT NUMBER: 01, do we need to put in column A "2" and then in column C "2" as well? 
We have been filing jointly for 12 years and have never had to mail in a hard copy, nor have we ever claimed any dependents or anyone claim us.
We appreciate your time.