I also have an issue with Ghost Hearts but it is only the Companion passives (Faithful, Vicious, etc.) that will not stick. I can choose other ranger abilities just fine. It seems to only be a Ghost Heart problem. I have tested this with single class and multiclass. With no subclass or the other subclasses I can choose any or all of the Companion passives and they work fine.
Another more minor issue: when I made a Paladin/Ranger (Shepherd), although I chose Paladin as the 1st class, Ranger would be first during Ability selection instead of Paladin. Also, although at the end of Character creation my class would read as Paladin first and Ranger below that, after loading into the game proper, under the Character Sheet, it would read as Ranger on top, with Paladin below that. I note it as I haven't seen that before with other multiclass characters I've made.