I came across this strange error, which baffled me for ages, but was simple to fix. I had duplicate resource references in web.xml and binding files.
com.ibm.ws.exception.RuntimeError
at com.ibm.ws.runtime.component.ApplicationMgrImpl.startApplication(ApplicationMgrImpl.java:328)
at com.ibm.ws.runtime.component.ApplicationMgrImpl.start(ApplicationMgrImpl.java:268)
at com.ibm.ws.runtime.component.ContainerImpl.startComponents(ContainerImpl.java:536)
at com.ibm.ws.runtime.component.ContainerImpl.start(ContainerImpl.java:413)
at com.ibm.ws.runtime.component.ApplicationServerImpl.start(ApplicationServerImpl.java:152)
at com.ibm.ws.runtime.component.ContainerImpl.startComponents(ContainerImpl.java:536)
at com.ibm.ws.runtime.component.ContainerImpl.start(ContainerImpl.java:413)
at com.ibm.ws.runtime.component.ServerImpl.start(ServerImpl.java:287)
at com.ibm.ws.runtime.WsServer.start(WsServer.java:128)
at com.ibm.ws.runtime.WsServer.main(WsServer.java:225)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:85)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:58)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:60)
at java.lang.reflect.Method.invoke(Method.java:391)
at com.ibm.ws.bootstrap.WSLauncher.run(WSLauncher.java:222)
at java.lang.Thread.run(Thread.java:570)
Caused by: java.lang.NullPointerException
at com.ibm.ejs.csi.ResRefListImpl.initializeIsolationLevel(ResRefListImpl.java:186)
at com.ibm.ejs.csi.ResRefListImpl.(ResRefListImpl.java:137)
at com.ibm.ws.webcontainer.metadata.WebMetaDataFactory.createMetaData(WebMetaDataFactory.java:123)
at com.ibm.ws.runtime.component.MetaDataMgrImpl.createFactoryMetaData(MetaDataMgrImpl.java:142)
at com.ibm.ws.runtime.component.MetaDataMgrImpl.createMetaData(MetaDataMgrImpl.java:186)
at com.ibm.ws.runtime.component.DeployedModuleImpl.start(DeployedModuleImpl.java:350)
at com.ibm.ws.runtime.component.DeployedApplicationImpl.start(DeployedApplicationImpl.java:578)
at com.ibm.ws.runtime.component.ApplicationMgrImpl.startApplication(ApplicationMgrImpl.java:311)
... 16 more
---- Begin backtrace for nested exception
java.lang.NullPointerException
at com.ibm.ejs.csi.ResRefListImpl.initializeIsolationLevel(ResRefListImpl.java:186)
at com.ibm.ejs.csi.ResRefListImpl.(ResRefListImpl.java:137)
at com.ibm.ws.webcontainer.metadata.WebMetaDataFactory.createMetaData(WebMetaDataFactory.java:123)
at com.ibm.ws.runtime.component.MetaDataMgrImpl.createFactoryMetaData(MetaDataMgrImpl.java:142)
at com.ibm.ws.runtime.component.MetaDataMgrImpl.createMetaData(MetaDataMgrImpl.java:186)
at com.ibm.ws.runtime.component.DeployedModuleImpl.start(DeployedModuleImpl.java:350)
at com.ibm.ws.runtime.component.DeployedApplicationImpl.start(DeployedApplicationImpl.java:578)
at com.ibm.ws.runtime.component.ApplicationMgrImpl.startApplication(ApplicationMgrImpl.java:311)
at com.ibm.ws.runtime.component.ApplicationMgrImpl.start(ApplicationMgrImpl.java:268)
at com.ibm.ws.runtime.component.ContainerImpl.startComponents(ContainerImpl.java:536)
at com.ibm.ws.runtime.component.ContainerImpl.start(ContainerImpl.java:413)
at com.ibm.ws.runtime.component.ApplicationServerImpl.start(ApplicationServerImpl.java:152)
at com.ibm.ws.runtime.component.ContainerImpl.startComponents(ContainerImpl.java:536)
at com.ibm.ws.runtime.component.ContainerImpl.start(ContainerImpl.java:413)
at com.ibm.ws.runtime.component.ServerImpl.start(ServerImpl.java:287)
at com.ibm.ws.runtime.WsServer.start(WsServer.java:128)
at com.ibm.ws.runtime.WsServer.main(WsServer.java:225)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:85)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:58)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:60)
at java.lang.reflect.Method.invoke(Method.java:391)
at com.ibm.ws.bootstrap.WSLauncher.run(WSLauncher.java:222)
at java.lang.Thread.run(Thread.java:570)