Most likely, the IRS received a copy of the form 1099-S that was issue for the sale. Instead of getting this form in January, after the close of the tax year, as you do other tax forms, it was included in your closing papers. Therefore the sale should have been reported on form 8949 and include with your tax filing. Form 8949 would have indicated the home sale exclusion, so that 0 capital gain was reported.
I suggest writing to the IRS to explain the situation; that this was the sale of your home, that you owned and lived in for more than 2 years of the 5 years prior to sale and that the gain was less than $100K.
