I worked for the same company last year in two different positions. One as an independent contractor(Form 1099) Jan-June, and as an employee from June to Dec (W-2). On my W-2 I have 2 exemptions, I should only have one (as single) I think I filed as head of household as well. On turbotax if I file as single, will that make a difference since my w-2 has 2 exemptions?
Also, turbo tax is prompting me to file a schedule C, which I don't think I should have to since that's profit/loss for a company and I was just an independent contractor not a business owner. When it asks me what the 1099 was for, I put wages and it asks me if I also received a w-2 from this company. I did but for a completely separate job that took place after the 1099 position was complete. Do I put that I received a w-2 from company or not since it was after the 1099 job was over?

I think you are confusing the withholding with the actual tax filing.

If you are single, file as single status and you will only have one exemption to claim (this is different to your tax withholding).

On the same tax return you will need to include your W2 and your 1099 income. You will need to file a Schedule C because being a contractor means that you are self employed. You will get to claim expenses.

W2 means wages as an employee, while 1099 means income as self employed person or independent contractor.

For difference between W2 and 1099, read
Your U.S. Tax Return: W2 or 1099: Employee or Independent Contractor. (http://taxipay.blogspot.com/2008/03/w2-or-1099-employee-or-independent.html)