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Currently the @webServiceRef annotation is defaultly injected into any target (java class) in EJB Project. This was implemented due to issue 99214. It should rather rely on InjectionTargetQuer.isInjectionTarget() method. See the : http://websvc.netbeans.org/source/browse/websvc/core/src/org/netbeans/modules/websvc/core/jaxws/actions/JaxWsCodeGenerator.java?r1=1.13&r2=1.14
Also: http://websvc.netbeans.org/source/browse/websvc/core/src/org/netbeans/modules/websvc/core/jaxws/actions/JaxWsCodeGenerator.java?r1=1.14&r2=1.15
Fixed. Diff: http://websvc.netbeans.org/source/browse/websvc/core/src/org/netbeans/modules/websvc/core/jaxws/actions/JaxWsCodeGenerator.java?r1=1.16&r2=1.17