Cancelling orders may not clear everything.
For example, after I order a ship to 'dock, do something (say, loot a crate), then (cancel orders and) order an 'escort in <OnOrdersCompleted>, the ship rotates to face my ship, but cannot move. I guess that the game still considers the AI ship docked. Again, with a looted crate example, the crate is empty but is still there. The ship gets unstuck if I destroy the crate or command it to [W]ait, then [F]orm up.
Missiles with passthrough multiply when reflected.
To see this, fire the Katana Star cannon at a Dwarg fortress or Zoanthrope Behemoth.
Mules and other unarmed autons should not reak & Attack.
Mules will join with the rest of your wingmen and/or combat autons when this order is given. I do not want such noncombatants to charge into a battle to die!
Bugs
Download and Play in 1.9 beta 1...
Drake Technologies (Alpha): More hardware for combat in parts 1 and 2!
Star Castle Arcade: Play a classic arcade game adventure, with or without more features (like powerups)!
Playership Drones: Buy or restore exotic ships to command!
Other playable mods from 1.8 and 1.7, waiting to be updated...
Godmode v3 (WIP): Dev/cheat tool compatible with D&O parts 1 or 2.
Drake Technologies (Alpha): More hardware for combat in parts 1 and 2!
Star Castle Arcade: Play a classic arcade game adventure, with or without more features (like powerups)!
Playership Drones: Buy or restore exotic ships to command!
Other playable mods from 1.8 and 1.7, waiting to be updated...
Godmode v3 (WIP): Dev/cheat tool compatible with D&O parts 1 or 2.
PM wrote: Mules and other unarmed autons should not reak & Attack.
Mules will join with the rest of your wingmen and/or combat autons when this order is given. I do not want such noncombatants to charge into a battle to die!
Damright!!
Dom 
I have this old save (and game version) with bug #2 being severily evidenced and causing crippling lag.
(func(Admin Response)= true){
if(admin func(amiable) = true)
Create func(Helpful Posts)
else func(Keep Calm and Post derisive topics)}
if(admin func(amiable) = true)
Create func(Helpful Posts)
else func(Keep Calm and Post derisive topics)}