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.

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.

My ships also flew outside the border and automatically turn around and come back in. In this state they are not controllable, which is ok.

The NPC ship just despawned.