Raphael,
I don't see a MultipleBagFetchException in the abbreviated stack trace you provided, but, do you have that exception in your server.log stack trace when you deploy your JARs and WARs?
If so, what do your entity objects (@Entity) look like? Do you have a situation where you are doing an EAGER fetch using a List collection?
I, too, used Glassfish and the toplink ORM did not have a problem with this. But, it looks like the Hibernate version with JBoss AS 7 does not accept this.