Systematic analysis is carried out for molecular phase in (omega(1),omega(3)) coherent control scheme. Two mechanisms for nonzero molecular phase are proposed. It is shown that the imaginary part of the three-photon transition operator, which is due to the contribution of the intermediate continuua, can give different phase factors for the one- and three-photon transition amplitudes, yielding very important effects of molecular phase in (omega(1),omega(3)) coherent control. We also show that the interactions between the final continuum states can result in nonzero molecular phase, when the intermediate states are discrete. These findings are discussed in relation to Gordon and co-workers' recent observations [Zhu er al., Science 270, 77 (1995)1 on phase lag. (C) 1997 American Institute of Physics.