Why would the IRS find something wrong with my return? Doesn't FreeTaxUSA calculate it correctly?

Your tax return is based on the information you enter. If you leave off income that the IRS knows you should've included, or if you claim a credit and the IRS determines you weren't allowed to claim it, they may automatically adjust your refund amount. Unfortunately, this can happen if you enter any inaccurate information into the FreeTaxUSA software.