While the facts are limited and the situation requires a fair amount of additional information, it appears your "former" employer paid you as if you were an employee.
W-2 wages do not go on Sch C. So if you followed the TT instructions for inputting your W-2, they will not be reported on Sch C. The "wages" should be showing up on your 1040 line 1.
You indicate that federal and state taxes were withheld.
Were FICA taxes withheld as well?
If they were, then as stated previously, the former employer continued to treat you as an employee.
If FICA was not withheld, then you have a problem which is beyond the scope of this forum. This means that the former employer most likely misclassified you and reported this incorrectly.
However, as noted earlier, there are many factors that need to be understood to determine the correct response.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
