Illegal access: this web application instance has been stopped already

Problem solved after restarting the tomcat and apache, the tomcat was caching older version of the app.

In short: this happens likely when you are hot-deploying webapps. For instance, your ide+development server hot-deploys a war again. Threads, that have been created previously are still running. But meanwhile their classloader/context is invalid and faces the IllegalAccessException / IllegalStateException becouse its orgininating webapp (the former runtime-environment) has been redeployed.

So, as states here, a restart does not permanently resolve this issue. Instead, it is better to find/implement a managed Thread Pool, s.th. like this to handle the termination of threads appropriately. In JavaEE you will use these ManagedThreadExeuctorServices. A similar opinion and reference here.

Examples for this are the EvictorThread of Apache Commons Pool, that "cleans" pooled instances according to the pool's configuration (max idle etc.).

I suspect that this occurs after an attempt to undeploy your app. Do you ever kill off that thread that you've initialised during the init() process ? I would do this in the corresponding destroy() method.