(The same problem as described in bug#159177, but for GlassFish. So different source files.)

When clicking on a blue line in the output window "GlassFish Server 3+", NetBeans may open a wrong file with the same name. Eg. when you use multiple versions of the same library for different projects.

I think, here's the problem:
In LogHyperLinkSupport.java
        @Override
        public void outputLineAction(OutputEvent ev) {
            FileObject sourceFile = GlobalPathRegistry.getDefault().findResource(path); 

The javadoc of findResource states
"In case more than one source root contains the resource, one is chosen arbitrarily."

That's not good. When more than one source root contains the resource, the user should be prompted to choose the right one.