"Did I miss a step? "
Yes. Stop looking at Wages & Income for actual tax information.
It is one of the peculiarities that TurboTax summary screens print the things you entered, whether or not they are taxable. This leads to understandable confusion. Always check for the actual information reported on the tax return itself.
Instead look at your 1040. There is no 1099-MISC line on the 1040 return, so that should not be there. There is, however, a line for Schedule E on Schedule 1 (line 5) of the 1040 - your royalties as reported on Schedule E (i.e., net of depletion) should be here.
As a reality check, manually add up your expected income and see if it matches line 9 on the 1040 - unless you had some subtractions from income on line 22 of Schedule 1, this should be a close match and should show that your royalties are not being double reported.
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