Created attachment 157915 [details]
The NetBeans project

To reproduce the problem:

1. Create a new project, type "Java EE, Enterprise Application".

2. Create a new database with Java DB. user app/app.

3. Create a new entity "user". Tick "Create Persistence Unit.

DataSource : "New Data Source. JNDI 
name : jdbc/testBug 
Database Connection : choose the new database created in the step 2.

4. Create an EJB session bean stateless.

5. In this EJB add a reference to an entity manager :

@PersistenceContext(unitName = "testBugGlassfish-resources-ejbPU")
    private EntityManager em;

    public void persist(Object object) {
        em.persist(object);
    }

6. Deploy the application.
Error message : Invalid resource : java:module/jdbc/testBug__pm

Remark : it works if the project is a "Java Web project" and not a "Java EE, Enterprise Application" (for a Java Web project glassfish-resources is used to define the datasource). (Petr Hejl solved it I think).

For an enterprise application glassfish-resources is in META-INF of the EJB module; for a Java Web project the file is in WEB-INF.