Damage to the Player's fighter is gone in the next part of a mission.
The damage repairs start before the player-character's hands push the buttons.
Even though communications should be encrypted, enemy communications can be heard.
A small prize crew should not be able to take control of a ship the size of the Victorum; even if the bridge is taken, the engineering section isn't.
Despite being in an asteroid field, the listening post has no shields.
How did the overseer jump when it was caught in a huge tractor beam?
For the mission to destroy the listening post, it would make far more sense to simply destroy the station rather than to destroy the receivers first.
During Mission 7, Frisk says that he has the 'cold sweat' on his neck. Transoshans are cold-blooded, and therefore do not sweat.
When the X-Wings first arrive at Foster Haven, Captain Jarves refers to the Player as 'pilot', even though there are a number of pilots in the area.