I have a limited knowledge of Class Action Cases but apparently there is often a lead Plaintiff that perhaps initiates the case prior to class certification by the federal court.
Here, perhaps Berkeley Insurance (and/or BB) was the lead Plaintiff and the reason they said to exclude Fannie was because they only hold mostly Freddie Mac JPS and/or common and Fannie Mae JPS.
The "contract" was the retainer agreement between the lead Plaintiff and the law firm and that contract excluded the law firm from including Fannie Mae Common.
Since they were "bankrolling" the initial Litigation prior to Class Certification then that could explain why the Fannie Mae Common was excluded.