My return is saying I'm self employed, why is it filing a self employed return, when my wife and I are both W2 employees?

Did you get a 1099Misc for something?  Is W2 box 13 checked for Statutory Employee?

Or because you have upgraded to the Self Employed version?
You can try to clear and start over  <a rel="nofollow" target="_blank" href="https://ttlc.intuit.com/replies/4248526">https://ttlc.intuit.com/replies/4248526</a>

no its not checked in box 13

You can simply use the "clear and start over" feature in the program.  Note that by doing so, it erases the current entries if there are any, but will keep the previous information from last year including your personal info, the income categories and the different schedules you have filed.  Follow the prompts and program will revisit those areas for clarification and assist you to select the appropriate version for your new tax return.  

1. Sign into your account, select Take me to my return

2.  To your left, select Tools, click on the drop-down menu

3. Select Clear and Start Over