Molecular phases are computed near the resonances in the (omega(1), omega(3)) coherent control scheme for excitations to predissociating final states. We show that the phase factors for the one-and three-photon transition amplitudes are identical, giving a vanishing molecular phase, when the intermediate manifolds consist only of discrete states and when the final continuum states do not interact. The phase lag between the dissociation products identically vanishes across the resonance in this case. On the other hand, when there is contribution of the intermediate continuum states, the imaginary part of the three-photon transition operator can give different phase factors for the one- and three-photon transition amplitudes, yielding very important effects of the molecular phase in (omega(1), omega(3)) coherent control. It is also shown that couplings between the final continuum states can give different molecular phase for different product channels in the absence of the effects of the intermediate continuum states, exhibiting the phase lag of the products near resonances. We demonstrate that the phase lag may show minimum near the top of the resonance, as was observed in Gordon and co-workers' recent observations [Zhu et al., Science 270, 77 (1995)] on the phase lag in HI coherent control experiments, indicating that the observed phase lag is due to the effects of the molecular phase.