The Anu were strongly influenced by their long years of rigorous training. While they were all becoming emotional, and mentally unstable, this expressed differently in the scientists and military parts of the crew.
The military third of the crew felt that humanity could not be trusted, and that the best course of action was to enslave all of them. The two thirds that were scientists disagreed. They argued that their mission was going badly, that they were making mistakes, and that they needed to turn around and go home – or at least get in touch with home and get someone who was not crazy over here to sort things out. Distrustful and paranoid, the military considered this very poor judgement.
The disagreement between them lasted for a long time, until it escalated.