Crew Members/Lifts Getting Stuck During Battle:
Caused by to many crew trying to repair a room at once. For instance, if you have your O2 room, and you have 3 crew with the orders to repair it if the health is < 100%. One of the crew will instead go to the room to the right of the O2 room and become unresponsive. If there is a Lift to the right of the room, the crew member will go one to the right of the lift, even if that means they go into your armor or half way up a floor. Even if they end up in a proper place, this will prevent the Lift from working anymore. This also seems to prevent crew from entering the original target room anymore as well.
Weapon Combo +Damage Still Applying When No Longer True:
If you upgrade your ship and it extends out the front of the ship. Any weapons that used to be touching the front of the ship will still retain their +10% combo damage, even if they are no longer touching the right side of the ship. You can even place new rooms in front of them and gain the +10% damage on those rooms as well. Unsure if this actually applies in combat, but the stats still show it as applying when looking at your ship.
Target Condition Room Bug:
If you have a command for a crew member along the lines of (If Room HP < 100) (Target Condition Room) and then after that have (None)(Target Origin Room). If a room then takes damage, the crew member will walk to the room as expected, but will then turn around and go straight back to the origin room without actually repairing anything. This will end up with the crew member uselessly moving back and forth between the rooms. This does not happen if you tell the crew member to target a specific room e.g. (If Shield Room < 100)(Target Shield Room).