If by net self-employment income you mean net profit minus the deductible portion of self-employment taxes, the result you are seeing is the result of marking the Maximize box for an individual 401(k) contribution. Either go back and tell TurboTax that you made a contribution to an individual 401(k) then unmark the Maximize box for that, or just switch to forms mode and remove that mark, leaving only the Maximize box for a SEP contribution marked.
