Don't enter a negative income amount. The IRS compares the total income reported on Schedule C to the total of the 1099-MISC forms that you received. If the total income that you report is less than the total of the 1099-MISC amounts the IRS will think that you did not report all your income.
You could enter the correction as a business expense. But why is the 1099-MISC wrong? Is it just a mistake, or did they include a payment they did make that you that you don't think should be included? If that's the issue, what was the payment for that you think should not be included in the 1099-MISC?
