How could Amanda appear in the live telecast of Logos and Akae. How did she know where it is being telecast from and how could she instantaneously reach there why it is going on, when Armaros and The Pilot couldn't find it so as to stop it. So many things go on and time lapses while the live telecast is still going on, that raises question about the entire real time flow of things.
Armaros' behavior towards The Pilot is odd. Armaros shouts at him, accuses him of inability to see or understand the gravity of the situation, sort of questions his competence and intentions. That is not the a way an employee can behave to a boss, let alone such a super boss.
Amanda's behavior was odd thought the entire movie. She just keep on questioning, doubting, irritating The Pilot endlessly. It is said that she is an Artificial Intelligence, so it is not clear why The Pilot made her like this and tolerated her. And if she didn't have free will how could download Helias' data and run away from The Pilot. It tells that she had free will, then what was she complaining about all the time.