I know the NEC form is new but I have had a number of these instances with Form 1099MISC when something was coded as subject to SE tax when it was not.  I had always paper filed with a statement explaining why the payment was not subject to SE tax.  In only one instance did the IRS respond with a notice.  In that case, I basically copied what was sent with the return originally and that one went away as well.

I had hoped to file electronically and yes, pay the Medicare tax as suggested by the administrator.  But as I said yesterday, I will suggest to my client that we paper file with a statement claiming the payment is not trade or business income and see what happens.