In general E and B field are not always in phase. They are in phase if there's no net free charge flow in the medium through which the wave propagates, example of such media are dielectric and vacuum (this one not really a medium though). If there is free charge fluctuation such as in conductors the wavevector wouldn't be real anymore (more precisely there is attenuation to the field) and magnetic and electric fields wouldn't be in phase.
Actually the response of material depends on the incoming field frequency, the determining quantity is σ/(εω) where σ, ε, and ω are conductivity, permittivity, and frequency respectively. The bigger that quantity the closer the material to behave as a conductor. For example water can behave as a conductor within certain frequency region.