Sometimes it's easier to debug Xcode problems by looking at the build log for the command lines it's using.
If you're building from the command line, you can get that message if you don't specify -miphoneos-version-min=
This compiles:
(where conftest.c just contains int main() {})
/Applications/Xcode5.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang -arch i386 --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.0.sdk --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator6.0.sdk -miphoneos-version-min=6.0 conftest.c
And this gives the error:
/Applications/Xcode5.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang -arch i386 --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.0.sdk --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.0.sdk conftest.c
ld: building for MacOSX, but linking against dylib built for iOS Simulator file '/Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator6.0.sdk/usr/lib/libSystem.dylib' for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)
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