"(The income was actually a schedule C loss of about $4.6K)"

Are you sure you are not confusing Gross Income and business Net? You don't "make" a loss. You still make Income.

You would not get a W2 and a 1099-NEC for the same income. And if they got a 1099-NEC for the income of that business, that typically is only a subset of the income they have for the business that year. It would be an error to enter the 1099-NEC and also their Gross Income, in other words.