The U.S. Government Accountability Office investigated NASA's program to build the Space Launch System and
the Orion spacecraft and released a report that recommends changes to how NASA assesses the cost and schedule risk of these programs.
According the GAO, there are both technical challenges (such as the heat shield for the Orion spacecraft) and management challenges. The two are related, of course, because "technical challenges could result in cost overruns and schedule delays."
For assessing the cost and schedule risk, NASA used a joint cost and schedule confidence level (JCL) analysis but followed few best practices for estimating cost and schedule. In particular, "the Orion cost estimate met or substantially met 7 of 20 best practices and its schedule estimate met or substantially met 1 of 8 best practices." The GAO concluded that "Without sound cost and schedule estimates, decision makers do not have a clear understanding of the cost and schedule risk" and recommended that NASA managers "perform an updated JCL analysis with cost and schedule estimates in line with best practices."
Links:
GAO report:
http://www.gao.gov/products/GAO-16-620Paper on JCL methodology:
http://arc.aiaa.org/doi/abs/10.2514/6.2013-5524