In the linear sigma model, the Lagrangian is given by
$$ \mathcal{L} = \frac{1}{2}\sum_{i=1}^{N} \left(\partial_\mu\phi^i\right)\left(\partial^\mu\phi^i\right) +\frac{1}{2}\mu^2\sum_{i=1}^{N}\left(\phi^i\right)^2-\frac{\lambda}{4}\left(\sum_{i=1}^{N}\left(\phi^i\right)^2\right)^2 \tag{11.65} $$ (for example see Peskin & Schroeder page 349).
When perturbatively computing the effective action for this Lagrangian the derivative $ \frac{\delta^2\mathcal{L}}{\delta\phi^k(x)\delta\phi^l(x)} $ needs to be computed. (for instance, Eq. (11.67) in P&S):
$$ \frac{\delta^2\mathcal{L}}{\delta\phi^k(x)\delta\phi^l(x)} ~=~ -\partial^2\delta^{kl} +\mu^2\delta^{kl}-\lambda\left[\phi^i\phi^i\delta^{kl}+2\phi^k\phi^l\right].\tag{11.67}$$
My question is, how is one supposed to handle the derivative term?
This seems to be completely implicit in the presentation of P&S, but from what I could gather it should go like so:
1) Because we are computing the effective action, $\mathcal{L}$ is actually under an integral and we can replace $\left(\partial_\mu\phi^i\right)\left(\partial_\mu\phi^i\right)$ with $-\left(\partial^\mu\partial_\mu\phi^i\right)\phi^i=-\left(\partial^2\phi^i\right)\phi^i$ using Stokes' theorem.
2) Then when performing the first derivative I get $\frac{\delta}{\delta\phi^l}\left[-\left(\partial^2\phi^i\right)\phi^i\right]=-\partial^2\phi^l$.
3) It is the second derivative I get stuck at, for as far as I can see, $\frac{\delta}{\delta\phi^k}\left[-\partial^2\phi^l\right]=0$, for there is only dependence on the 2nd derivative of $\phi^l$ and not $\phi^l$ itself. If, as is usual in field theory, the field and its derivatives are treated as independent dynamical variables, then the second derivative should also be an independent dynamical variable. How is it explained then, that the result of this computation should be $\frac{\delta}{\delta\phi^k}\left[-\partial^2\phi^l\right]=-\delta^{kl}\partial^2$?