When running jlink and the module being linked in contains a manifest with the main-class:

> jar --create --file=modules/hello.world.jar --main-class=com.greetings.HelloWorld -C build/hello.world .

and you run jlink with --strip-native-commands, then jlink will attempt to strip the file hello.world (a shell script on Mac) that does not exist. Without a manifest it works fine.