Novel two-dimensional (2D) layered materials, such as MoS2, have recently gained a significant traction, chiefly due to their tunable electronic and optical properties. A major attribute that affects the tunability is the number of layers in the system. Another important, but often overlooked aspect is the stacking configuration between the layers, which can modify their electro-optic properties through changes in internal symmetries and interlayer interactions. This demands a thorough understanding of interlayer stacking configurations of these materials before they can be used in devices. Here, we investigate the spatial distribution of various stacking configurations and variations in interlayer interactions in few-layered MoS2 flakes probed through the low-frequency Raman spectroscopy, which we establish as a versatile imaging tool for this purpose. Some interesting anomalies in MoS2 layer stacking, which we propose to be caused by defects, wrinkles or twist between the layers, are also reported here. These types of anomalies, which can severely affect the properties of these materials can be detected through low-frequency Raman imaging. Our findings provide useful insights for understanding various structure-dependent properties of 2D materials that could be of great importance for the development of future electro-optic devices, quantum devices and energy harvesting systems.