The launch check that checks almost nobody
The escape-shuttle rule is meant to be "all living crew members and Jones must be aboard the Narcissus". But LaunchGate's loop steps 8 bytes from the wrong column after the first living crew member, so in practice the launch only requires the first-listed living crew member (plus Jones) to be aboard — and a later crew member standing in Airlock #1 bogusly blocks it. Verified in the simulator.
The harpoon gun that destroys the ship's inventory
When the harpoon gun is fired at the Android, the item-wipe loop at CrewHitsAndroid has an inverted final compare versus the alien-side version: it destroys every item in the game except those lying loose in the room — everything held by anyone, anywhere, is wiped — and the Android itself takes no wound. Verified in the simulator.
The scare bonus that can never happen
AlienScareCheck is supposed to grant a bonus when the crew member is armed with a serious weapon, but the test requires two mutually exclusive equality checks to both pass, so the bonus is unreachable.