Yes I agree, as Christophe says, that an application-managed persistence contexts must be managed by the application(as its name says

)
Additionally, when a JTA application-managed entity manager is used, if the entity manager is created outside the scope of the current JTA transaction, it is the responsibility of the application to associate the entity manager with the transaction (if desired) by calling EntityManager.joinTransaction.
For resource local transactions, the entity manager should start and commit the transaction by itself. Please see "5.7 Application-managed Persistence Contexts" of ejb-3_0-fr-spec-persistence.