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.
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 immediately, before the helmsman actually obeys the order after initially protesting and aborts the jump. Normally in Wing Commander a jump point wormhole opens just as a ship enters it and stays open until it passes through.
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.