If your royalties are for Mineral Rights, they should be reported on Schedule E, for Rentals and Royalties, and you won't be subject to SE tax. If your royalties were payment for intellectual property that you created, such as music royalties or book royalties, then they would be reported on Schedule C, and you'd pay SE tax on them.
Go back to your 1099-MISC for the royalties and make sure that you entered it properly. The income should have been reported in Box 2.
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