If you save and quit with a Defense Drone active, it may remain active even after a jump, using up no power, and is invisible, though it still shoots down missiles. Stays active even when unequipped and reequipped.
When restarting a game that started with a human female crew member, the crew member might turn male, but the name remains the same.
The automated fueling scout that has a chance of appearing if you run out of fuel may have different dialogue and options if you reload the game.
The "No Escape" Achievement for the Crystal Cruiser does not work as intended. It is awarded even when you trap 4 of your own crew in a single room on an enemy ship (with lockdown ability, the lockdown bomb needs to be tested) (last checked on v. 1.01.). It also awards if any of the crew assembled are drones.
When you get a weapon reward from killing an enemy crew if they at the same time sent a missile and destroy your teleporter it actually gives you double the said weapon.
The "Trustworthy Auto-Pilot" achievement may sometimes be earned by killing the crew of an enemy ship in a beacon close to a star.
If you activate Cloak right when an enemy's weapon is about to fire, it could freeze the weapon rendering it useless and unable to fire.
If the enemy ship is destroyed immediately after launching a Boarding Drone, and the exploding animation finishes just as the drone enters your ship screen, the drone will freeze in mid-air and is not recoverable with Drone Recovery Arm.
If you save and reload on the empty beacon with a quarantine message repeating endlessly, one of your crew may die for no reason.
If you are at a shop that offers a Drone Control that comes with a System Repair Drone (for 75 scrap), if you save and reload it will change to have a Defense Drone Mark I instead (for 85 scrap).
Turning off the oxygen system may immediately remove all oxygen from the ship (which can be disastrous for most crew, of course).
Firing Chain Weapons whilst having Weapon Reloader augmentation installed may cause fire delay for non-Chain weapon such as Ion Stunner to actually increase with each barrage of Chain weapons, whose delay will decrease. This seem to correlate upon how weapons are placed in weapon tray.
In GNU/Linux operating system with FTL in full screen mode, Workspaces and Alt + Tab do not work unless Shift + Tab is first engaged to open the Steam overlay first.
In GNU/Linux, using Shift + Tab to open the Steam overlay can cause FTL to stop "listening" to the keyboard.
There is a UI issue where, in the event that FTL is not listening to the keyboard, there is no way to close the game without using Ctrl + Alt + Del (Windows) / Activity Monitor (OS X) / SIGKILL in tty (Linux).
Pirate ships do not take electrical debuff in nebula, and are not affected by the Pilot being taken out in FTL jumps.
In Crystal Cruiser type B, during a cloak, the outline looks like a Zoltan Cruiser. Fixed in 1.02
In the Crystal sector, a random event that involves saving a Crystal ship from pirates may give you a "Crystal Shard" weapon as reward. This weapon has no sprite in the equipment menu and "Should Never See This Description." as description. Fixed in 1.02
It's possible to go through blast doors by commanding your crew member to go into the next room, then into the room behind that one, and back again. Fixed in 1.03
If your ship is in Danger (Asteroid Fields, Sun) you cannot open your ship info Screen. By using the hotkey (U) it is still possible. Fixed in 1.03.3
While you have a Drone Recovery Arm, if you activate a Hull Repair Drone and jump to another beacon before the drone is destroyed, the drone isn't used up and you still heal. Fixed in Advanced Edition.
If you beat any phase of the boss, all its weapons will become Triple Heavy Lasers. However, when you beat it again, they return to normal. Fixed in Advanced Edition.