The 1099-MISC is no longer used to report non-employee wages/income. There is a new form that reports what use to be reported in Box 7 of the 1099-MISC. Take another look at your return, Box 3 of the 1099-MISC would not be treating the income as self-employment. Self-employment income or non-employee income is now reported on the new form 1099-NEC.
If it is calculating self-employment then try deleting the 1099-MISC and re-enter it. Box 3 of 1099-MISC income should end up on Schedule 1, Line 8z Other Income.
