I suspect the issue will go away if you restart the service:
Quit Xcode, Instruments, and the iOS Simulator and then run this in Terminal.app:
killall -9 com.apple.CoreSimulator.CoreSimulatorService
I have not seen an issue like this before where the device itself really is duplicated in the run destinations list. Other reports have been that there really were duplicated devices (with unique UDIDs), but in your case, you are seeing duplicates of the exact same device.
If the issue is continuing to reproduce, please enable debug logging:
defaults write com.apple.iphonesimulator DebugLogging -bool YES
defaults write com.apple.CoreSimulator DebugLogging -bool YES
Reproduce the issue with debug logging enabled, and then file a bug report at http://bugreport.apple.com including ~/Library/Logs/CoreSimulator/*.log and /var/log/system.log.
If you have any idea how you got into this state, please share it.
EDIT:
Based on discussion in comments, the issue was caused by adding the iOS 7.1 SDK (not the simulator SDK, the device SDK). This is not a supported configuration, but it is certainly odd that doing so caused this issue. Please note that you should always build against the newest SDK and just set the deployment target to the minimum version you wish to deploy to.
Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs
may did something with this issue? – Obcordate