I had the same problem in Xcode 6.1.1. I did the following to solve it:

1. Set the configuration file setting* "None" for the Pods related target.
2. Close the .xcworkspace.
3. run pod install again
4. now open and build your .xcworkspace

*The configuration file setting is found by selecting the project (not the target) and then the Info tab.

xcode pod install 安装失败，提示缺少文件