Her SEP contribution is entirely independent of the 401(k) contributions. One does not affect the other.
Her SEP contribution is limited to 20% of net earnings from self-employment. Net earnings are net profit minus the deductible portion of self-employment taxes. Marking the Maximize box for a SEP contribution will cause TurboTax to automatically calculate this. Make sure that there was no experimentation with individual 401(k) entries. If the result on Schedule 1 line 16 is not the correct SEP contribution, try deleting the Keogh, SEP and SIMPLE Contribution Worksheet and revisiting the self-employed retirement section to re-mark the Maximize box for a SEP plan.
Make sure that the only entries made related to the 401(k) are the entries in box 12 of TurboTax's W-2 form, code D for elective deferrals, code AA for Roth contributions. Enter these nowhere else.
