It seems that the Employer has reported more 1099-Misc income to you may have received in 2008. This is not an unusual situation and the way to handle this is to report this income (as it appears on the 1099-Misc) on Schedule C Line 1.
Then I suggest that you claim an expense item called "additional income erroneously reported" under the category called "Other Expenses". I would then attach a statement to the tax return explaining that the Employer has erroneously reported the additional income to you in 2008 for which you have claimed the deduction under the Other Expenses category. You don't really have to call the IRS or get stressed up about this, this is a very common occurrence!
