Xcode6:Embedded binary is not signed with the same certificate as the parent app
I had to select my app under 'Targets', then go to the 'Capabilities' tab and click 'Fix Issues' under the 'App Groups' section
I had discrepancies under Code Signing. My Extension and Main app had different certificates selected. Once I set both to use distribution it worked fine.
In the case of using WatchKit, make sure that your Watch App has the correct "Team" selected in the Watch App Target settings (under General > Signing > Team). I had set the phone app's team, but not the watch app's team.