The deadliest tangles wrapped around a companies Enterprise Systems often result from the structure of the organisation. Individual departments and operational functions depend upon small efficiencies generated by the existing systems. A replacement system might represent a dramatic improvement in overall efficiency but would almost certainly disrupt the existing organisation. Project like that can only be led from the top of an organisation - without that level of leadership the IT function is confined to continuing the development of those small efficiencies to the detriment of the whole.
You see it everywhere I am afraid.