The data corresponds to the characterization of various point defects and grain boundaries in rotationally commensurate MoS2 on epitaxial graphene. The MoS2 was grown on the epitaxial graphene on silicon carbide using chemical vapor deposition. The structural and electronic nature of the defects are investigated using scanning tunneling microscopy and spectroscopy. This work gives insight into common defects in MoS2 in efforts to guide defect engineering for tailoring the performance of MoS2/graphene heterostructure. DOI: 10.1021/acs.jpcc.6b02073