It's likely that the IRS is not figuring the additional tax on the difference between the two W-2s but is considering the entire correct W-2 to be missing from your tax return and the incorrect W-2 included with your tax return as being reportable income in addition to that on the missing W-2 (with the IRS assuming that the employer failed to provide the IRS with a copy of the W-2 that you did report). This would be in line with the procedures in the Internal Revenue Manual; if the filed tax return does not include a W-2 that matches what they received directly from the employer, assume that the W-2 that they received from the employer was simply omitted when you prepared your tax return.
As xmasbaby0 indicated, you'll likely need to provide an amended tax return to correct and explain the error on your originally filed tax return so that the IRS can match the reporting on your tax return with the reporting that they received.
