Numerical studies of the waveguide properties of liquid crystal layers bounded by substrates with indium tin oxide (ITO) electrodes using the finite difference time-domain (FDTD) method are carried out. On the basis of the experimental transmittance spectra of ITO-coated glass substrates in the visible and near-infrared ranges, a Lorentz model describing the dielectric properties of the ITO electrodes is created. Then, by numerical modeling, optical systems including a homogeneously aligned LC layer between the thin alignment films and the ITO electrodes on the quartz substrates are studied. It is shown that, in the case of the use of traditional alignment films or their absence, the ITO electrodes lead to significant resonant losses in the waveguide mode for both TE- and TM-polarized light. The losses mechanism based on a phase-synchronized mode coupling occurring in relatively narrow spectral ranges is discussed. We also propose a method to control and exclude the losses using thin alignment films with a proper thickness and low refractive index.