When I tested entering Form 1099-MISC separately as an oil, gas minerals or copyrights or patents royalty on Form 1099-MISC, I had to then go to the Rental section.
I did see the depletion automatically calculated. But, where the depletion expense was then listed, I could click the trash can icon next to it to delete it.
If you are saying you do not have this option at all, I recommend deleting Form 1099-MISC and re-entering it.
Depletion is automatically calculated at 15% and is not subject to self-employment tax when reported on Schedule E. Without knowing the full context of your circumstances for the mineral rights, it may or may not be appropriate to decline this expense.
For more information, see Publication 525 Taxable and Nontaxable income re: Depletion
Publication 535 Business Expenses: Who Can Claim Depletion?
