Hello,
When playing with a race which scavenges such as the Snathi Revenge and a ship carrying a citizen of an enemy civilization is killed and its ship scavenge this leads to a "Lost Citizen" message which blocks the game from proceeding further. I would suggest converting the ship to an unarmed scout as part of the scavenging process.
Similarly, a trade ship of an enemy civilization is scavenged, it cannot be used as a trade ship because it doesn't have a home port defined. I would suggest copying the home port of one of the ships doing the scavenging and if it's not possible (because the ship doing the scavenging is a Bazar ship, then use either the nearest planet of the scavenging civilization or the home world.