L. Michelle Bennett and Howard Gadlin, "Supporting interdisciplinary collaboration: The role of the institution," in Michael O’Rourke et al, Enhancing Communication and Collaboration in Interdisciplinary Research, Sage, July, 2013,356-84, argue that institutional support is critical to successful interdisciplinary collaboration. They identify five common problems: lack of institutional self-awareness, lack of organizational trust, failure of leadership, mismanagement of difference, and mishandling conflict. They provide numerous examples.
Other chapters in that volume also address challenges in administering interdisciplinary initiatives.