How organizational structure and conflict relate to each other.
Teamwork requires cooperation and communication.  When you have diverse teams with different job tasks and goals, then conflict will arise.  In some cases this conflict will benefit the organization by motivating each team to work harder in competition with one another (Ivancevich et al, 2008).  However this can also backfire and cause anti productive behaviors between the teams.  If key factors are missing, then the conflict will often consume both teams and lead to failure (Sheard & Kakabadse, 2001).  
Key factors like clear goals for each time, clear leadership, good communication, appropriate resources and infrastructure are needed for success.  Without these factors conflict among teams can become disruptive (Sheard & Kakabadse, 2001).
If the organization has the foresight to design the teams and interaction with intelligence, then conflict can be reduced (van der Helm, 2007).  I have teams that are organized by floor in a large facility.  Each team is responsible for their own area, yet they have a reciprocal independence amongst each other.  The success of each team and the completion of their work relies upon the output of the other floors.  This can cause conflict if one floor perceives another as slacking or giving them inferior materials.  One of the techniques used to alleviate conflicts is common goals and objectives for all teams and variable rewards for achieving those goals. We have also provided better communication tools and training in conflict resolution so they can manage relatively minor issues independently without management involvement.  This has dramatically reduced the number of disciplines and productivity problems.
Chong, P., & Benli, O. (2005). Consensus in team decision making involving resource allocation. Management Decision, 43(9), 1147-1160.
Drea, C., & Carter, A.P. (2009). Cooperative problem solving in a social carnovore. Animal Behavior, 78, 967-977.
Ivancevich, J.M., Konopaske, R., & Matteson, M.T. (2008). Organizational Behavior Management. New York, NY: McGraw-Hill/Irwin
Sheard, A.G., & Kakabadse, A.P. (2001). From loose groups to effective teams. The Journal of Management and Development, 21(2), 133-155
van der Helm, R. (2007). Ten insolvable dilemmas of participation and why foresight has to deal with them. Foresight, 9(3), 1-17.