hibernate insert to a collection causes a delete then all the items in the collection to be inserted again

I highly suspect that you're not overriding equals and hashCode properly. Wrongly overriding them can lead to the kind of behavior you're experiencing (as the hash key is used as keys in maps). Double check what you did with equals and hashCode.

Using your annotated entities with good equals and hashCode, this code (logically equivalent):

Session session = HibernateUtil.beginTransaction();
Employee emp = (Employee) session.load(Employee.class, 1L);
CohortGroup group = (CohortGroup) session.load(CohortGroup.class, 1L);
group.getMembers().add(emp);
emp.getMemberGroup().add(group); // set the other side too!!
session.saveOrUpdate(group);
HibernateUtil.commitTransaction();

produces the following output on my machine:

08:10:32.426 [main] DEBUG o.h.e.d.AbstractFlushingEventListener - processing flush-time cascades
08:10:32.431 [main] DEBUG o.h.e.d.AbstractFlushingEventListener - dirty checking collections
08:10:32.432 [main] DEBUG org.hibernate.engine.CollectionEntry - Collection dirty: [com.stackoverflow.q2649145.CohortGroup.members#1]
08:10:32.432 [main] DEBUG org.hibernate.engine.CollectionEntry - Collection dirty: [com.stackoverflow.q2649145.Employee.memberGroup#1]
08:10:32.443 [main] DEBUG org.hibernate.engine.Collections - Collection found: [com.stackoverflow.q2649145.CohortGroup.members#1], was: [com.stackoverflow.q2649145.CohortGroup.members#1] (initialized)
08:10:32.448 [main] DEBUG org.hibernate.engine.Collections - Collection found: [com.stackoverflow.q2649145.Employee.memberGroup#1], was: [com.stackoverflow.q2649145.Employee.memberGroup#1] (uninitialized)
08:10:32.460 [main] DEBUG o.h.e.d.AbstractFlushingEventListener - Flushed: 0 insertions, 0 updates, 0 deletions to 2 objects
08:10:32.461 [main] DEBUG o.h.e.d.AbstractFlushingEventListener - Flushed: 0 (re)creations, 2 updates, 0 removals to 2 collections
08:10:32.463 [main] DEBUG org.hibernate.pretty.Printer - listing entities:
08:10:32.473 [main] DEBUG org.hibernate.pretty.Printer - com.stackoverflow.q2649145.CohortGroup{id=1, members=[com.stackoverflow.q2649145.Employee#1]}
08:10:32.474 [main] DEBUG org.hibernate.pretty.Printer - com.stackoverflow.q2649145.Employee{id=1, memberGroup=}
08:10:32.474 [main] DEBUG o.h.p.c.AbstractCollectionPersister - Inserting collection: [com.stackoverflow.q2649145.CohortGroup.members#1]
08:10:32.480 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
08:10:32.491 [main] DEBUG org.hibernate.SQL - insert into MYSITE_RES_COHORT_GROUP_STAFF (COHORT_GROUPID, USERID) values (?, ?)
Hibernate: insert into MYSITE_RES_COHORT_GROUP_STAFF (COHORT_GROUPID, USERID) values (?, ?)
08:10:32.496 [main] TRACE org.hibernate.type.LongType - binding '1' to parameter: 1
08:10:32.497 [main] TRACE org.hibernate.type.LongType - binding '1' to parameter: 2
08:10:32.499 [main] DEBUG o.h.p.c.AbstractCollectionPersister - done inserting collection: 1 rows inserted

No delete before the insert!

By the way, note that you should set the link on both sides when working with bi-directional associations, like I did on the group and on the employee.

Or add defensive link management methods on your classes, for example on CohortGroup:

public void addToMembers(Employee emp) {
    this.getMembers().add(emp);
    emp.getMemberGroup().add(this);
}

public void removeFromMembers(Employee emp) {
    this.getMembers().remove(emp);
    emp.getMemberGroup().remove(this);
}

I had this same problem and with some trial and error found that the deletes did not occur if I used a Set instead of a List as my collection. Irritating, given that I'm using JSF and the UI components will only iterate over Lists. But there it is.