Bound states in the continuum (BICs) in photonic crystals represent the unique solutions of wave equations possessing an infinite quality-factor. We design a type of bilayer photonic crystal and study the influence of symmetry and coupling between TE and TM polarizations on BICs. The BIC modes possess $C_{3v}$ symmetry in the x-y plane while the mirror-flip symmetry in the z-direction is broken, and they provide selective coupling into different layers by varying frequency. The enhanced TE-TM coupling due to broken mirror-flip symmetry in the z-direction gives rise to high-Q factor BIC states with unique spatial characteristics. We show the emergence of such BIC states even in the presence of coupling between the TE- and TM-like modes, which is different from the existing single polarization BIC models. We propose to study BICs in multilayer systems, and the results may be helpful in designing photonic settings to observe and manipulate BICs with various symmetries and polarizations for practical applications.