When I try to stop tomcat8 on Java 8, I get a few memory leaks errors:
org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web applic
There is nothing to worry about. This is a standard message tomcat outputs when it detects the application has started it's own Thread or created a ThreadLocal. If you terminate the thread on shutdown and remove the threadlocals when they are no longer needed, then there will be no problem.
Why would I get all this memory leaks errors? as well, when I run shutdown, it doesn't shut it down, I have to manually kill the process.
I've seen this behavior, when an application has started ScheduledExecutor (but this will happen with any other Thread/TheadPool) and didn't shut it down on contextDestroyed. So check if you are shutting down your threads on application/server stop.
Now on your concrete problem why the server doesn't stop:
JDBC drivers are registered in the JVM as singletons, and are shared with all webapps. More info here. The best solution to your problem is to move the MySQL driver in Tomcat's /lib folder. If you cannot do that you can try this but it's more like a hack than a real solution.