It is well known that the Hong-Ou-Mandel (HOM) effect can be realized on beam splitters (BSs) in the form of coupled waveguides. It is believed that in this case, the theory is similar to HOM interference on conventional BSs. In this work, it is shown that if a BS is used in the form of a coupled waveguide, the theory of HOM interference can differ significantly from the known one. It is shown that even in the case of completely identical photons, the visibility of V can essentially differ from unity. The developed theory must be taken into account in quantum optical schemes, where BSs are represented mainly as coupled waveguides.