Let an EM wave propagate in the $\hat{z}$ direction - $$\vec{E_I}(z,t)=E_0e^{i(kz-\omega t)}\hat{x}$$ it hits a conducting surface at $z=0$ so there is a reflected wave - $$\vec{E_R}(z,t)=E_{0R}e^{i(-kz-\omega t)}\hat{x}$$ Since the total field must vanish on the conducting surface we conclude that - $$E_{0R}=E_0e^{i\pi}$$ However, if the conducting plane was placed at $z=L$ we would find - $$E_{0R}=E_0e^{i(2kL+\pi)}$$ It appears that the phase difference (which is physical?) between the incoming and reflected wave is arbitrary. On the other hand, our choice of coordinates is also arbitrary. As far as the waves are concerned, the position of the conducting plane should not matter at all, so there is an apparent conflict.
Edit: We found the two waves to be - $$\vec{E_I}(z,t)=E_0e^{i(kz-\omega t)}\hat{x}$$ $$\vec{E_R}(z,t)=E_0e^{i(k(2L-z)-\omega t + \pi)}\hat{x}$$ Their sum is a standing wave - $$\vec{E_I}(z,t) + \vec{E_R}(z,t)= E_0(e^{i(kz-\omega t)} + e^{i(k(2L-z)-\omega t + \pi)})\hat{x}= E_0e^{i(kL-\omega t)}(e^{ik(z-L)} - e^{-ik(z-L)})\hat{x}= 2iE_0e^{i(kL-\omega t)}\sin(k(z-L))\hat{x}$$ And the difference in their phases is - $$\Delta \phi(x)=2k(L-z)+\pi$$ which at $z=L$ comes out as $\pi$ so the boundary conditions are satisfied. However in some other points the phase difference is not $\pi$
Edit2: If the reflected wave gains only an additional phase $\pi$ an immediate conclusion is that the wavenumber must be quantised. This is odd, because if the surface is moved just a little bit further away, the standing wave will be destroyed. This will lead to a violation of the boundary conditions at the interface.