Banned in Germany: In Wing Commander IV, the scene where Seether slits Captain Paulson's throat has two versions, with and without gushing blood. The latter is the one found on the German release of the game.
While the voice actor for Merlin, the Rapier's onboard AI in the movie, wasn't listed in the credits (a question mark was put where the actor's name would have been), it turns out that Merlin was voiced by none other than Mark Hamill, who played Blair in the games Wing Commander III and Wing Commander IV.
Prophecy was supposed to have the glowy bits at the ends of the Tiamat's arms work like the shipkiller plasma cannon mounted on the Kraken, but time constraints resulted in the feature never being implemented.
In the sequel, Secret Ops, the Murphy class destroyers were supposed to have an anti-capship gun mounted in the nose, but again time constraints lead to it being cut. The barrel of the planned gun is still visible on the model, but it's not functional, leaving the destroyer with its pathetic laser turret armament as the only thing backing up the handful of fighters it could carry.
Working Title: The proposal for what eventually became Wing Commander was named "Squadron".note A nod to this is featured in the single player portion of Star Citizen, titled "Squadron 42.