In the quest "Underground Undercover" you have to eventually warn Desdemona about an attack on the railraod HQ by the Brotherhood of Steel. This activtes as soons as you are given the order to kill desdemona by Father. You are able to tell her that you've been ordered to kill her but are not able to warn her about the attack, which means you are unable to complete the main story through the railroad. All she does is repeat the same 5 lines of dialouge when I talk to her when I'm supposed to be able to have a conversation with her.