In this paper, it is demonstrated that the calculated physical adsorption energies, substrate–adsorbent distances and substrate distortions strongly depend on the size of the employed supercell and particularly on the type of optimization in the case of very flexible two-dimensional monolayers, such as indium (II) selenide (InSe). It has been established that calculations with optimization of only atomic positions and calculations with optimization of atomic positions and lattice parameters can give energies of different signs and values. In-plane (stretching and compression) and out-of-plane (ripple formation) distortions also lead to significant changes in the calculated adsorption energies. The influence of substrate flexibility and adsorption on the electronic structure and optical properties is also discussed.