1099-NEC from non-profit organization for that work does not fit IRS definition of independent contractor

Hello TT tax experts,

My daughter does administrative operations work for a non-profit organization that is not yet tax-exempt (though has plans to get this status). Her work is directed by the organization's executive director, with whom she meets weekly to get direction on both what she does and how.  She performs some duties, on her own as that process has been established with the exec director's input, e.g. paying invoices.  She is paid hourly, which vary from week to week.  

 

She received a 1099-NEC, which invokes the self-employment tax.  However, to my read, she does not meet the IRS criteria for an independent contractor (see below). Apparently, the non-profit organization is not set up with structure for employees and does not pay social security and medicare taxes.

 

>>>> Does my daughter owe the self-employment tax despite not meeting the definition of an independent contract simply because she works for a non-profit?

 

>>>> Should I dispute the NEC (independent contractor) classification by filing IRS form SS-8?

 

She's raised the issue with her boss, the Exec Director, and the accounting firm but it won't be resolved before 4/15.

 

https://www.irs.gov/businesses/small-businesses-self-employed/independent-contractor-defined"You are not an independent contractor if you perform services that can be controlled by an employer (what will be done and how it will be done). This applies even if you are given freedom of action. What matters is that the employer has the legal right to control the details of how the services are performed."
 
Thank you!!