Banned in China: 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.
Executive Meddling: Hobbes' betrayal in Wing Commander III was apparently because Chris Roberts didn't like the idea of a Kilrathi good guy.
Seether in Wing Commander IV was also Warren Keffer on Babylon 5. Wait, who? Well, he was that network-mandated pilot guy in the second season who got his name on the opening titles, was given as little screentime as possible and they Dropped a Bridge on Him at the earliest possibility.
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, Wing Commander IV, and Prophecy.
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.
Deleted Scene: There was a traitor subplot cut from the final release due to poor audience reception at a test screening, but several scenes earlier in the final cut of the movie rely on the subplot to make sense. The Novelization of the film includes the subplot, and as a result the story flows more smoothly.
Vindicated by Cable: Wing Commander was a bomb at the box office, not helped by its limited release, but video rental income has made good the production costs, and given its regular airing on cable channels (particularly non-US ones) even has something of a genuine fandom.* as opposed to a So Bad, It's Good one Although all are pretty Vanilla, there have been three releases of the film, two on DVD (non-anamorphic and anamorphic) and one on Blu-ray.
The Series Bible indicates that later seasons would have had a Kilrathi pilot joining the crew, with all the tension that would bring, and the show's plot would run right up to the beginning of Wing Commander III, incorporating plot elements from the second and third games.
The show was originally intended to be a prequel leading into Wing Commander III: The Heart of the Tiger, complete with younger versions of all of the game's characters. Though the concept was reworked considerably before the show was produced, you can still see many similarities in the form of numerous expies amongst the crew, as well as using Wing Commander III uniforms instead of the ones seen in the very first game (which was set shortly after the show's setting).