My 1099-MISC was additional services for my employer yet it keeps coming up as Self-Employment which keeps requiring me to complete a Schedule C?

Since it's from your employer, it really should be on your W2 with the correct withholding taken out for social security and medicare tax.  I would start by requesting a corrected W2.  If you get nowhere with that request, I would enter it as Other Reportable Income under the Miscellaneous Income section.  

Follow these steps:  

1. Sign in to TurboTax,
2. Click on Federal Taxes at the top of the screen; 
3. Go to Wages and Income; 
4. Toward the bottom, you will see a box to click that says Add More Income.   
5. Scroll down the page to the last section titled: Less Common Income and click show more; 
6. Select start or update next to the last topic titled Miscellaneous Income, 1099-A, 1099-C; 
7. Scroll down to the last option titled Other reportable income and select Start or Edit; 
8. Click Start next to Other income not already reported on a Form W2 or Form 1099; 
9. Click YES to Did you receive any other wages; 
10. Continue past Wages earned as a Household Employee, Sick or Disability Pay, Medicaid Waiver Pay and select YES again to the question Any Other Earned Income?
11. Select Employee Compensation that was not reported on a W2; 
12. Continue answering all questions.  The Reason Code you should use is H; 
13. Then click Done.