This is a known bug affecting iOS 8.x and 9.x. You can work around it by creating /usr/lib/swift directories in the relevant simulator runtime root.
Downloaded simulator runtimes are located in /Library/Developer/CoreSimulator/Profiles/Runtimes.
For example, to fix the iOS 9.3 simulator:
sudo mkdir '/Library/Developer/CoreSimulator/Profiles/Runtimes/iOS 9.3.simruntime/Contents/Resources/RuntimeRoot/usr/lib/swift'