It has been speculated that small guest molecules such as Ar, Kr, N-2, and O-2 may doubly occupy the large cages of the type II structure of clathrate hydrate. In this study we examined this possibility on Ar hydrate with molecular dynamics calculations. It was found that the total energy and pressure of the system increased significantly when the large cages were doubly occupied. Furthermore, even though Ar clathrate with double occupancy may be stabilized by external pressure, the cubic structure is severely distorted. Owing to restricted empty space, the motions of the Ar atoms in doubly occupied large cages are highly correlated and give a unique stretch vibrational band that can be used for characterization.