If you don't travel to Cassiopeia immediately after getting this quest, Sarah will ask you "Next stop Cassiopeia ?" at every location you visit in the meantime. She will also continue to ask this when you temporarily leave Cassiopeia before having completed all of the quest objectives there. Thus, we can safely assume that this dialogue line is tied to a location change event and that it also checks whether the new location is Cassiopeia. What it does apparently not check for, however, is the right quest stage to stop it from being spoken: she will continue to ask this at every location you visit after completing the tasks at Cassiopeia and before speaking to Admiral Logan, even upon arriving at New Atlantis while on your way to Admiral Logan. At this point in the quest, asking this makes no sense anymore because there's nothing left to do at Cassiopeia.