Maniac and Vagabond don't wear any medal ribbons on their Confed uniforms, when in the previous game they did. Yet Blair still does, the same amount as he had before (3). Eisen and Tolwyn also have medals, each a slightly higher amount than they did before.
Maniac's rank insignia is the wrong way round in when the Intrepid's systems suddenly shut down when they arrive in the Peleus system.
Maniac's rank insignia is the wrong way round and has moved an inch sideways when Eisen is saying that he's leaving the Intrepid to take his evidence to Confed.
During the early missions where Blair and Eisen are with Confed, if the player ejects, a cutscene plays where Eisen rebukes Blair via a video screen in the ejection pod, but he is wearing a Border Worlds uniform instead of a Confed one.
The lower row of medal ribbons on Eisen's Confed uniform change to the other way around when Paulsen arrives on the Lexington and remain this way from this point onwards.
After telling Blair he's worked out what the Flashpak is, Pliers exits by starting to climb up a ladder which is supposed to lead to another level on the ship. But as the camera moves away he can be seen coming back down again after only going up one step, giving away that the ladder leads to nowhere and the actor was only pretending to go up it.
Bulldog clip on cord attached to the back of Bob-O-Matte's helmet visible when a group of Banshees are ambushed by Excaliburs.
When Blair and the other pilots on the Lexington watch a news interview with Admiral Tolwyn, a close-up shot of the screen shows that it is clearly a 1990s Panasonic cathode-ray tube television. The story is set in the 27th century. Although it's been placed inside some casing, the whole front of the TV is undisguised and the Panasonic logo and buttons can be seen. In other scenes TVs and monitors are better disguised.
Once again, as in the previous game, Paladin is listed in the credits as "Maj. James 'Paladin' Taggart" (Maj. means Major). He was only a Major in the first game, in Wing Commander II he is a Colonel, in Wing Commander III he is a General, and in this game he is retired from the military and is now a senator.
When Tolwyn orders the Vesuvius helmsman to turn the ship around just as it's about to go through a jump point, the jump wormhole starts to open but closes again before the helmsman actually obeys the order and aborts the jump after initially protesting. Normally in Wing Commander a jump point wormhole opens just as a ship enters it and stays open until it passes through.
Blair says "We represent the Union of Border Worlds and Rear Admiral Wilford" instead of Vice Admiral Wilford in the cutscene that plays if the player chooses to fly to Telamon using a Vindicator rather than a Dragon.
The triangular badge below Vagabond's name tag is askew when Blair first meets him aboard the Lexington.