According to Internal Revenue Service information reporting specialist Schroff, #100-5950, it is permissible for a company to issue both a W-2 and a 1099 to the same individual in a case where the individual is an employee (reported on a W-2), but also works as a contractor on a project outside of their regular employee duties/hours (reported on a 1099).
Schroff gave the following example: the owner of a shoe-making facility hires Joe to make shoes for 40 hours a week. Joe also has carpentry skills and the owner contracts with Joe to build an addition to his shop, which Joe does on the weekends. The owner issues a W-2 to Joe for his work as a shoe-making employee, and a 1099 for his contract carpentry work. So it is permissible to issue both a W-2 and a 1099 to the same individual. Given proper documentation, there should be no consequences for the individual. We recommend that you look carefully at the guidelines for determining employee versus contractor status (see 1099 Basics: Independent contractor or employee).