Depends on how you entered the 1099 income ... if it ended up on the Sch 1 line 8 (and the amount is more than $400) then the IRS expected it to be reported on a Sch C and the self employment taxes paid on the profit. If you did not put the amount on the Sch C then the form SE was not produced. So if you have no expenses against this 1099 income to report and the IRS has already figured the SE taxes you can simply go ahead and pay them. If you want to stand your ground that this did not belong on a Sch C then you will have to explain why to the IRS.
