There has also been reports of terrorist activity and sabotage from other crew members who did not agree with the senior staff on topics of survival within the Andromeda Galaxy. After this conflict, the crew on board who had rebelled were banished from the Nexus and labeled as ' Exiles'.

With its original leadership decimated in the Scourge disaster shortly after arrival, and unable to establish contact with any of the First Wave Arks, the staff on board began having disputes, this eventually led to a rebellion against the Nexus leaders. The Nexus was activated a year before the Hyperion arrived in Andromeda. The arks are to dock with the station on its central support column to provide it with extra power and storage. Upon reaching Andromeda, construction is due to commence on the station in order to give it a Presidium-like central torus and another Ward-like superstructure. At launch, the Nexus resembles two Wards of the Citadel joined together at the base.