Defects, which are an unavoidable component of the material preparation process, can have a significant impact on the properties of two-dimensional devices. In this work, we investigated theoretically the effects of different types and positions of point defects on band alignment and transport properties of metallic 1T-phase MoS2/semiconducting 2H-phase MoS2 junctions. We found that the Schottky barriers of junctions depend on the type of defects and their locations while showing anisotropic characteristics along the zigzag and armchair directions of 2H-phase MoS2. Moreover, defects in the central scattering region can generate local impurity states and introduce new transmission peaks, while defects at the interface do not generate impurity-state-related transmission peaks. Together, these defect-related peaks and Schottky barriers jointly affect the transport properties of the junctions. Understanding the complex behaviors of defects in devices can make the process of material preparation more efficient by avoiding harm.