Suppose one has a real scalar field $\phi$ and its conjugate momentum field $\pi := \partial_t \phi$. If the scalar is free and using metric $(-+++)$, the action is $$ \int d^4x\ \mathscr{L}_{\mathrm{free}} = - \frac{1}{2} \int d^4 x\ ( \partial_\mu \phi \partial^{\mu} \phi + m^2 \phi^2 ) $$ which means the free Hamiltonian is $$ H_{\mathrm{free}} = \frac{1}{2} \int d^3 \mathbf{x}\ \big( \pi^2 + ( - \nabla^2 + m^2 ) \phi \ \big) \ . $$
My question is: For what reason is it not allowed that $H_{\mathrm{free}}$ includes terms of the form $\pi \phi$? I can see how this is related to $\partial_t(\phi^2)$, and feel like this may be why, but can't quite see the reason.