Enterprise resource planning (ERP) System is being used for the last 15 to 20 years and This research paper attempts to identify and explore the main issues affecting large scale businesses as well as small and medium scale businesses regarding the implementation of ERP System in enterprises. In this paper manufacturing companies are ranging in size from million dollars to over billion dollars as per their annual turnover. Basically, this research paper highlights the main issues where the different methods or solutions are to be applied according to the organization's scale. Except this also the benefits get differed by company size as small and medium companies gets some limitations compared with large companies. Large companies get financial improvement and economically better results whereas these smaller and mid-size organizations get better results in Production as well Logistics and manufacturing sectors.