Two suggestions. The first is that perhaps the JVM is in fact not running, but whatever you’re using to tail your console or log output is just lagging behind on updating. The second is that perhaps the JVM is just taking a while to shutdown. I’ve seen servers kept alive for up to 20-30 seconds after the server has stopped responding to web requests due to a hanging JVM shutdown hook that was keeping it running for a bit.
Start by confirming if the java process is still running. If it is, grab a thread dump with
jstack -l PID to see what it’s doing. You may just need to be more patient.