However: In respect of the children you should keep the profile of their biological father. As long the connection is marked as an ex to the mother the profile will not be visible when having the focus on her or her family's profiles.
You should also respect it if the children or his family want to build the tree on his profile.
Step children and foster children are really not realised well enough in Geni yet.
I don't quite know what has happened in your case, but i think that maybe your stepson was linked not to you, but to some relationship, and once you've changed it (but adding your ex) that relationship got distorted...