While trying to provide an answer to this question, I got confused with something which I think might be the root of the problem. In the paper the OP was reading, the author writes $$\frac{d\hat{A}}{dt}=\frac{\partial \hat{A}}{\partial t}+\sum_k \frac{\partial \hat{A}}{\partial x_k}\frac{dx_k}{dt}$$
for an observable $\hat{A}$. The author says that this chain rule expansion may be made, as well as the same thing but in momentum, but one may not have both at the same time, which was the source of OP's question. I argued that this was essentially a matter of function definition, and the fact that you can't have an observable depending on both position and momentum, because the operators of which these quantities are eigenvalues don't commute. But that raised the question which I came to pose here: what does it mean for the operator to depend on the $x_i$ or on the $p_i$? Is it something like $$\hat{A}: \Gamma \rightarrow Hom(H)$$ where the operator is mapping points in the phase space to observables in the Hilbert space? If so, is that meaningful? What is the interplay of the phase space here? My confusion lies in the fact that points in phase space as far as my understanding go would correspond to the eigenvalues of the position and momenta operators, and as such can I talk about them meaningfully in this way seeing as they do not commute? Furthermore, what is the meaning of $$\frac{\partial \hat{A}}{\partial x_i}$$
Essentially, what I'm asking about is: how does one define precisely the dependence of an operator on the "classical" degrees of freedom of a system and their conjugate momenta?
EDIT
Following d_b's answer, supposing that the derivative is taken in a classical setting and only then does quantization occur, take as an example the Hamiltonian for a 3D particle in some potential, $$H(x_i,p_i)=\frac{p^2}{2m}+V(x_i)$$
surely we'd all agree that $$\frac{dH}{dt}=\sum_k \frac{\partial H}{\partial x_k}\dot{x_k}+\frac{\partial H}{\partial p_k}\dot{p_k}$$
then "putting a hat on top of it" wouldn't alter the dependence on the $p$'s.
So either this isn't what's meant, or somehow the act of quantization removes one dependence or the other, which I can't see how.