Just seen this warning in my configuration:

• hibernate-entitymanager-4.3.0.Final
• hibernate-jpa-2.1.api-1.0.0.Final
• hibernate-validator-5.0.2.Final

It happens when calling ValidatorImpl.validate(...) which in turn calls Persistence.getProviders()

I believe the issue comes from the loadResolverClasses method in
CachinePersistenceProviderResolver

javax.persistence.spi.PersistenceProviderResolverHolder$PersistenceProviderResolverPerClassLoader$CachingPersistenceProviderResolver Line 145:
//keep Hibernate atop
if ( s.endsWith( "HibernatePersistence" ) && resolverClasses.size() > 0 ) {

Together with the PersistenceProvider containing both references this pushes the deprecated version on top of the new version.