Remus knows about Pattons..."Habits." And he doesn't really mind them. In fact, he uses these habits to his advantage to spread the intrusive thoughts. Considering that only Patton, Remus, and Deceit know about Pattons "Activities", there would be a reason for Remus to give Thomas those thoughts. It slowly gets easier and easier for Remus to get to Thomas after Patton starts worrying that his cover is going to be blown.
