In The Captain Is Dead Episode 2: Adrift, do all systems with any damage gain damage no matter where hostile aliens are?
What that means is that if an alien is in a room with a system that is damaged such as engineering and the teleporter has damage then another damage token will be added to the teleporter. If the comm system also had damage to it but there are no aliens on the bridge then no damage tokens will be added to it when the aliens cause the teleporter to get another damage token. What is happening is that the aliens are just causing more damage in the area they currently are.