I've copy & pasted example from http://www.doctrine-project.org/projects/orm/1.2/docs/manual/defining-models/1_0#relationships:join-table-associations:self-referencing-nest-relations:non-equal-nest-relations .
I've created User backend module using doctrine:generate-admin backend User task. On how to reproduce the error:
1. Add 3 User objects (A,B,C)
2. Open generated edit form for User A.
3. Set User B as Children from Children list and Save
4. Set User B and C as Chidren from Children list and Save
As a result you will see only C set as Children, and strange situation in database :
parent_id | child_id
pk_B | pk_B (!!!)
pk_A | pk_C