Why is the app automatically categorizing my income as professional, rather than business, and won't allow me to enter cost of goods sold/subcontract deductions?

If your self-employment income is from a T4A slip on Box 048, then you can go back to the slip and change your selection for the question “Source of box 48”.

To edit your T4A(P) Statement of Canada Pension Plan Benefits in TurboTax Online, search for “T4A” on the Tax Home page (2024 tax return on the left).