Note that not only the domain of integration but also the integrand depend on $x$. Let's (for a moment) write $F(x) = \int_x^0 f(x, t)\,dt = -\int_0^x f(x,t)\,dt$ for your integral. To handle the "double" $x$-dependence, we write $F$ as the composition of $\Delta\colon \mathbb R \to \mathbb R^2$, $x\mapsto (x,x)$ and $\Phi\colon \mathbb R^2 \to \mathbb R$, $(x_1, x_2) \mapsto -\int_0^{x_1} f(x_2, t)\, dt$. We have $F = \Phi \circ \Delta$, hence
$$ F'(x) = \nabla \Phi \bigl(\Delta(x)\bigr) \cdot \Delta'(x) $$
by the chain rule. Now $\Delta'(x) = (1,1)$, and
\begin{align*}
\partial_1\Phi(x_1, x_2) &= -f(x_2, x_1)\\
\partial_2\Phi(x_1, x_2) &= -\int_0^{x_1} \partial_{x_2} f(x_2, t)\, dt
\end{align*}
(for the first derivative we used the fundamental theorem). Plugin everything together, we obtain
$$ F'(x) = -f(x,x) - \int_0^x \partial_x f(x,t)\, dt $$