I have sometimes found a bit of a bug in the software. When you go through the questions about whether the property falls under exempt because it was a primary residence, sometimes I had to answer No to the question about living in it and then the software would give the correct exempt status. I would suggest you go through your return and see what happens when you tell the software it was not a residence.
If you already filed, then amend the return and make sure it reflects the correct exemption. If you have not filed, see if that makes it correct. It has been like that for years. It must have been a primary residence and lived in for at least two of the last five years before being sold.
