When you have to protect the flagship, assign the attack priorities and then destroy the two enemy ships, one of the ships fled. When I tried to hunt it down, it flew over the edge of the map and vanished. I was in a state, where you cannot continue the mission, because you have to destroy the ship, that vanished.
[Report] Enemy ships vanishes in Prologue
Happened to me too right now... looks like it just "despawns" outside the border.
If i remember correctly in BFG:A1 the ships would "bounce" outside the border and move back in.