Collection items (marked with orphanRemoval=true) are not removed from the database correctly if
1. the collection is not initialized
2. we now call ->clear() on it.
I think the problem is that PersistentCollection::clear() iterates through the uninitialized collection which is empty in this case. Thus the scheduleOrphanRemoval() method is never called.
The best example is within the doctrine 2 documentation: http://www.doctrine-project.org/docs/orm/2.0/en/reference/working-with-associations.html#orphan-removal . Calling $this->addresses->clear() raises this bug.
I'm currently helping myself by fixing the situation with accessing the elements of the collection before calling ->clear().