We present an analysis of the electronic properties of an MoS2 monolayer (ML) and bilayer (BL) as-grown on a highly ordered pyrolytic graphite (HOPG) substrate by physical vapour deposition (PVD), using lab-based angle-resolved photoemission spectroscopy (ARPES) supported by scanning tunnelling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) for morphology and elemental assessments, respectively. Despite the presence of multiple domains (causing in-plane rotational disorder) and structural defects, electronic band dispersions were clearly observed, reflecting the high density of electronic states along the high symmetry directions of MoS2 single crystal domains. In particular, the thickness dependent direct-to-indirect band gap transition previously reported only for MoS2 layers obtained by exfoliation or via epitaxial growth processes, was found to be also accessible in our PVD grown MoS2 samples. At the same time, electronic gap states were detected, and attributed mainly to structural defects in the 2D layers. Finally, we discuss and clarify the role of the electronic gap states and the interlayer coupling in controlling the energy level alignment at the MoS2/substrate interface.