Phase transitions in systems of adsorbed molecules on corrugated surfaces are studied by means of Monte Carlo simulation. Particularly, we have studied the phase diagram of D2 on graphite as a function of coverage and temperature. We have demonstrated the existence of an intermediate gamma-phase between the commensurate and incommensurate phase stabilized by defects. Special attention has been given to the study of the epitaxial rotation angles of the different phases. Available experimental data is in agreement with the simulations and with a general theory for the epitaxial rotation which takes into account defect stabilized situations.