from:http://stackoverflow.com/questions/25165016/cant-get-to-work-cocoapods-and-yosemite
In case someone else got the same issue, I did this to fix my issue:
Update Gems
1sudo gem update --systemUninstalled xpreproj
1sudo gem uninstall xpreprojMake sure to select All versions
Uninstalled Cocoapods
1sudo gem uninstall cocoapodsInstall xpreproj
1sudo gem install xpreprojInstall cocoapods
1sudo gem install cocoapodsRun
1pod --version to test.