To reproduce the issue:

mkdir a; touch test a/test
jdk-9/bin/jar cf test.jar -C a test test

Creating test.jar will fail (which is expected), but a temporary file be left behind.

$ mkdir a; touch test a/test
$ ls -l /tmp/test.jar*
ls: cannot access /tmp/test.jar*: No such file or directory

$ jdk-9/bin/jar cf test.jar -C a test test
java.util.zip.ZipException: duplicate entry: test
at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:231)
at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
at jdk.jartool/sun.tools.jar.Main.addFile(Main.java:1179)
at jdk.jartool/sun.tools.jar.Main.create(Main.java:849)
at jdk.jartool/sun.tools.jar.Main.run(Main.java:308)
at jdk.jartool/sun.tools.jar.Main.main(Main.java:1651)

$ ls /tmp/test.jar*
/tmp/test.jar16981332899083569432.jar