We just got this issue as well with 4.2.8.Final:

java.lang.ArrayIndexOutOfBoundsException: 3942
at org.hibernate.engine.internal.EntityEntryContext.reentrantSafeEntityEntries(EntityEntryContext.java:217)
at org.hibernate.engine.internal.StatefulPersistenceContext.reentrantSafeEntityEntries(StatefulPersistenceContext.java:1243)
at org.hibernate.event.internal.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:151)
at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:89)
at org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:61)
at org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1130)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1187)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
at org.hibernate.ejb.QueryImpl.getResultList(QueryImpl.java:268)