In deriving the LSZ formula, a crucial step is to show $$\langle|a_{p}^{\dagger}|\rangle=-i\int dx^0 \int \mathrm{d}^{3} x \partial_{0}\langle | e^{-i p\cdot x} \overleftrightarrow{\partial_{0}} \phi(x)|\rangle=-i\int d^4x e^{-ip\cdot x}(\square+m^2)\langle|\phi|\rangle$$ where for conciseness, I omitted the arguments in $\langle|,|\rangle$. But, from our experience with QFT, the creation operator can equally well be represented by the field operator $\phi(x)$ and its canonical conjugate $\Pi(x)$. $$a_{p}^{\dagger}=-i \int d^{3} x e^{-i p \cdot x}\left[\Pi(x)+i E_{p} \phi(x)\right].$$ Then, using Hamilton's equations for fields $$\begin{aligned} &\partial_{0} \phi(x)=\frac{\delta \mathcal{H}}{\delta \Pi(x)}=\Pi(x), \\ &\partial_{0} \Pi(x)=-\frac{\delta \mathcal{H}}{\delta \phi(x)}=\left(\nabla^{2}-m^{2}\right) \phi(x) \end{aligned}$$ we would have $$\begin{align} \partial_{0}(e^{-ip\cdot x}\left[\Pi+i E_{p} \phi\right]) =&- ie^{-ip\cdot x}E_p \left[\Pi+i E_{p} \phi\right]+e^{-i p\cdot x}\left[(\nabla^2-m^2)\phi+iE_p \Pi\right]\\ =&e^{-ip\cdot x}(E_p^2+\nabla^2-m^2)\phi=e^{-ip\cdot x}(-\partial^2/\partial t^2+\nabla^2-m^2)\phi \\=&-e^{-ip\cdot x}(\square+m^2)\phi \end{align}.$$ Notice the extra minus sign!
On the other hand $$\partial_{0} \left[e^{-i p\cdot x} \overleftrightarrow{\partial_{0}} \phi(x)\right]=e^{-ip\cdot x}(-E_p^2-\nabla^2+m^2)\phi=e^{-ip\cdot x}(\square+m^2)\phi$$ as desired. This is the correct result to be used.
As is apparent, I'm rather careless about these calculations, so hopefully nothing goes seriously messed. Assuming that is the case, these two expressions are clearly different by a minus sign! What is the origin for this discrepancy and how should we interpret this result?
This question emerges as I work my way through the QFT book by Gelis (section 1.5 specifically), the book might contain more relevant details, in case one finds my re-expression of materials makes no sense at all.