Many big organizations who are in existence since before the term agile came into existence are pursuing agile transformations and trying to integrate it with their existing structure. It has been an accepted fact that agile integrations are difficult in big organizations and many of such organizations fail the transformations. This is especially true for multisite software organizations where a traditional mix of old and new ways of working ends up creating issues. The result of such failure is the implementation of a hybrid way of working which ultimately leads to lower output and higher cost for the organizations.This paper looks at the integration challenges for multisite software engineering organizations and correlates with the theoretical findings by earlier with practical findings using survey and interviews as data collection tools. This paper specifically focusses on integration challenges involving self-organizing teams, power distribution, knowledge hiding and knowledge sharing, communications and decision making. The paper also has empirical evidence that shows that there is a communication and understanding gap between the employees and management in basic understanding of agile concepts.