Look at your Form 1040. What line shows the income, Line 7 (wages) or Line 12?. If it is on Line 12, you have entered it correctly.
You might want to call the IRS. They got the idea somehow you you were an employee. You may have forgotten some small job you did or there may be some other type of mix-up. It is always better to bite the bullet and make the call to clear things up asap. IRS 1-800-829-1040.