You may still wind up paying Self Employment tax on this income. You can object to this, though, when you file your tax return.
After you enter your 1099-MISC, you will answer questions that follow. On the screen Does one of these uncommon situations apply? check "Your employer reported this extra money on a 1099-MISC, but it should have been reported on a W-2."
On the next screen, you will see information about filing form 8919 to report this income. One of the indications noted in the Learn More link is "You formerly worked for this company as an employee and you are performing services in a substantially similar capacity and under substantially similar direction and control."
You will still have to pay what would have been your share of Social Security and Medicare taxes withheld from normal wages.
See this link to the IRS discussion of Employee vs Independent Contractor: https://www.irs.gov/businesses/small-businesses-self-employed/independent-contractor-self-employed-o...
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