That sounds like what is supposed to happen. This occurs when you have a "non-qualified" deferred compensation plan. (A qualified plan would be reported on a 1099-R.). The employer is supposed to withhold and pay the payroll taxes (social security, medicare) at the time the income was earned (when you did the work). Then the income is subject to income tax when it is actually paid to you. Since the employment taxes have already been paid, this is "other income" and not subject to self-employment tax and does not require a schedule C. It is not considered income "earned" from working (that happened when you earned it, not when you are paid).
Enter the 1099-MISC in the correct section. Answer No to all the special circumstances. Answer NO to all the testing questions (not earned from working, not like your regular job, did not receive similar money in the past of future). These answers are necessary to prevent Turbotax from treating the money as earned income and creating a schedule C.
