It seems that you might have separately entered the contributions in the self-employed retirement section of TurboTax. TurboTax gets the necessary amounts from the code-R entry in box 13 of the the Schedule K-1 (Form 1065) and your entries in the Schedule K-1 section as to how this contribution is broken into employee and employer contributions, so you must not enter them under Business Deductions and Credits.
I suggest deleting TurboTax's Keogh, SEP and Simple Contribution Worksheet and letting it auto-regenerate from the Schedule K-1 information.
