I encounter the same problem using these dependencies:
compile 'mysql:mysql-connector-java:5.1.23'
compile 'org.hibernate:hibernate-entitymanager:4.3.5.Final'
compile 'org.hibernate:hibernate-envers:4.3.5.Final'

(At the moment I am not using any envers-related stuff. The whole application consists of one Entity (Employee), a main class (PersistenceApplication) and the persistence.xml file:

<persistence version="2.1"
xmlns="http://xmlns.jcp.org/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence http://xmlns.jcp.org/xml/ns/persistence/persistence_2_1.xsd">
<persistence-unit name="pu">
<provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>

<class>com.example.Employee</class>
<properties>
<property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver" />
<property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost:3306/datenhaltung" />
<property name="javax.persistence.jdbc.user" value="root" />
<property name="javax.persistence.jdbc.password" value="root" />
<property name="javax.persistence.schema-generation.database.action"
value="drop-and-create" />
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQLDialect" />
</properties>
</persistence-unit>
</persistence>

The test program is fairly simple:

package com.example;

import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.Persistence;

public class PersistenceApplication {

	public static void main(String[] args) {
		EntityManagerFactory emf = Persistence
				.createEntityManagerFactory("pu");
		insertEmployee(emf, new Long(1), "Person 1");
		insertEmployee(emf, new Long(2), "Person 2");
	}

	private static void insertEmployee(EntityManagerFactory emf, Long id,
			String name) {
		EntityManager em = emf.createEntityManager();
		em.getTransaction().begin();
		Employee emp = new Employee(id, name);
		em.persist(emp);
		em.getTransaction().commit();
	}
}

package com.example;

import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;

@Entity
public class Employee {
	@Id
	private Long id;

	@Column
	private String name;

	protected Employee() {
	}

	public Employee(Long id, String name) {
		this.id = id;
		this.name = name;
	}

	public Long getId() {
		return id;
	}

	public String getName() {
		return name;
	}
}

As you can see, the message is also logged 3 times:

Apr 21, 2014 9:11:59 AM org.hibernate.ejb.HibernatePersistence logDeprecation
WARN: HHH015016: Encountered a deprecated javax.persistence.spi.PersistenceProvider [org.hibernate.ejb.HibernatePersistence]; use [org.hibernate.jpa.HibernatePersistenceProvider] instead.
Apr 21, 2014 9:11:59 AM org.hibernate.ejb.HibernatePersistence logDeprecation
WARN: HHH015016: Encountered a deprecated javax.persistence.spi.PersistenceProvider [org.hibernate.ejb.HibernatePersistence]; use [org.hibernate.jpa.HibernatePersistenceProvider] instead.
Apr 21, 2014 9:11:59 AM org.hibernate.ejb.HibernatePersistence logDeprecation
WARN: HHH015016: Encountered a deprecated javax.persistence.spi.PersistenceProvider [org.hibernate.ejb.HibernatePersistence]; use [org.hibernate.jpa.HibernatePersistenceProvider] instead.
Apr 21, 2014 9:12:00 AM org.hibernate.jpa.internal.util.LogHelper logPersistenceUnitInformation

if you need any further information, don't hesitate to ask..

regards,

Andreas