Derivative of a logarithm (chain rule)
\begin{eqnarray} \frac{\partial }{\partial \theta} \left[-y \ln\left(\frac{1}{1+e^{-\theta x}}\right)\right]&=&\frac{\partial }{\partial \theta} \left[y \ln\left(1+e^{-\theta x}\right)\right] \\ &=& -\frac{y x e^{- \theta x}}{1+e^{- \theta x}} \color{red}{\frac{e^{\theta x}}{e^{\theta x}}} \\ &=& -\frac{y x}{1 + e^{\color{red}{+}\theta x}} \end{eqnarray}
You are right and Mathematica is wrong !