In Star Fox 64's ancillary material, Planet Aquas is said to be an entirely water planet with its surface 100% covered by oceans. Star Fox Command however, would contradict this by showing there to be islands on Aquas in the Slippy's Resolve ending; Command's official Japanese guidebook even claims that Aquas' surface is now only 80% comprised of oceans.

In a Q&A with Takaya Imamura in 2023 on this subject, he theorized that perhaps, somewhere in-between the events of Star Fox 64 and Star Fox Command, the islands were created by underwater volcanic belts within Aquas' oceans, likening it to the emergence of Nishinoshima, a volcanic island in the Ogasawara Archipelago.

Hidden in the files for Star Fox 64 are what seem to be remnants of an unused first-person turret mode. Several files reference a stage with the initials "SB", with its header file, fox_sb_poly.h, being titled "スター ブレード 擬き" (Sutā burēdo ki). This translates to "Star Blade Imitation", named after the 1991 on-rails space shooter by Namco, where the ship's guns can only be used in first-person. Dylan Cuthbert and other developers of the original Star Fox admitted to being heavily inspired by Star Blade, claiming that one of their main goals was to recreate the experience of the game.

The file, fox_play.h, defines 3 scroll types of levels: corridor, all-range mode, and "JYUZA", or "銃座モード" (Jūza mōdo), which translates to "Gun turret mode". This file also defines five player modes: ARWING, TANK, SUB, HUMAN, and P_JYUZA, While the SB stage is listed with the other corridor stages, it still specifies that it's in the "JYUZA" category. The SB stage itself appears to be a shortened copy of the Area 6 stage devoid of any content except for one Moras enemy, suggesting that it and other stages were meant to be played in the turret mode during development.

In the game's source code, stages such as "SB", "CL" or "Colony", and Area 6 are subtitled "Great Fox", suggesting that the Great Fox mothership was also intended to use the turret mode. It would likely have been about firing lasers and guns from the ship while trying not to take damage, as there is a string for the ship's health bar named gfox_life. The game's levels, such as the Landmaster stages, are organized into overlay groups to save on memory; Area 6 strangely isn't grouped within the turret mode stages, but Sector Y is.

This unused game mode was restored via a fanmade patch on October 30, 2024, taking a few liberties to make up for the missing code and assets.

In the files for Star Fox 64 found in the 2020 Nintendo Gigaleak are references and assets for what appears to be a scrapped level named "Battleship". The string fox_map.c interchangeably calls it "Battleship", "Giant Battleship", and "Ground Ship"; it's possible that the latter could be a mistranslation of "Grand Ship", as they're spelled the same way in Japanese. The stage used a full 3D model, like Area 6 and Bolse, as its icon on the map selection screen. Its intended location was where Sector Y currently sits on the Lylat map selection screen, which is the hard path taken from Corneria, and its two branching pathways were known to be Zoness on the hard route and "Fortuna" (Fichina) on the normal route. According to the string fox_play.h, it was an all-range mode stage, and the audio_game.h string makes it appear that it was going to reuse Bolse's theme for its background music, implying that there would have been multiple phases for the level. This stage also had its own enemy data file, implying that it would have featured other enemy ships of some sort.

In October 2024, a group of modders and hackers responsible for the Star Fox 64 Decompilation Project were able to recreate this discarded stage via a fanmade patch.

The game's opening features the phrase "Star Fox in Nintendo 64". This was a translation error and is supposed to read "Star Fox on Nintendo 64". This was fixed in the 3DS remake.

The official Japanese Star Fox 64 guidebook reveals that Pigma Dengar, who became a subordinate of Andross, was effectively the real mastermind behind the creation of Star Wolf: he goated and manipulated Wolf into becoming its leader and also working for Andross as a means to combat the newly formed Star Fox team led by Fox McCloud, taking advantage of Wolf's supposed honorable, "magnaimous" side and also his prior rivalry with Fox's father, James McCloud. It is said that he manipulates the entire team behind the scenes in accordance to Andross' orders. It also reveals that Pigma had already been working underneath Andross during his time as a researcher at the Corneria Defense Force Scientific Research Institute. It's also revealed that both Pigma and Andross had custom engineered the Wolfens that the Star Wolf team utilize in their battles against the Star Fox team's Arwings.

In Super Smash Bros. 4, the trophies for Pigma and the Wolfen would reiterate this information, as would the official guidebook for Star Fox Command. The Star Fox 64 Official Player's Guide would similarly allude to Pigma being the root cause of Fox and Wolf's rivalry, claiming that, without his influence, perhaps they could have been friends in another timeline.

Prior to Star Fox Zero, there were two attempts in previous installments to revitalize the concept of the Walker from Star Fox 2, or at least the idea of the Arwing transforming into a robot form, those specifically being Star Fox 64 and Star Fox Command, games that both aimed at preserving ideas from the then-long-lost Star Fox 2.

• For Star Fox 64, according to Shigeru Miyamoto in an interview at the end of the Star Fox 64 Official Player's Guide, he wanted to have the Arwing transform into "a human-type craft". This was rejected by other staff members of the SF64 development team. In response, Miyamoto told his team to come up with better ideas, and from there they created the Landmaster and Blue Marine for additional vehicles.

• For Star Fox Command, according to Takaya Imamura in an interview in 2007, the dev team experimented with having the Arwing and other spacecraft transform into robots, but this was ultimately dropped.

Katt Monroe, a female feline character who first appeared in Star Fox 64, had undergone a notable change in appearance from that game going into Star Fox Command, most notably now having black fur instead of pink. According to Takaya Imamura in a 2011 Nintendo Dream magazine interview, he changed her appearance to be more "fashionable".

On the Japanese website for Star Fox 64, Slippy mentions certain background characters who would appear in future installments:

• Peppy's wife, Vivian Hare. According to Slippy, Peppy took her to planet Zoness for their honeymoon, which explains why Peppy is so distraught at its polluted status in SF64. Vivian would appear in-game for the first time in Star Fox Command, where it's revealed that she and Peppy had a daughter named Lucy, and that Vivian had died of a disease several years prior.

• Slippy's father, Beltino Toad. According to Slippy, Beltino works as an engineer for Space Dynamics, the manufacturer of the Arwing and many of the other vehicles the Star Fox team utilize. Beltino would later appear in-game for the first time in Star Fox Assault, and would later appear in Star Fox Command.

It's worth pointing that unlike Vivian, Beltino was mentioned in western ancillary SF64 material, that being both the official western Star Fox 64 website and the Star Fox 64 Official Player's Guide, where it states that he helped his son Slippy create the Blue Marine.

Much like the original Star Fox on Super Nintendo, Star Fox 64's stages are split into three difficulty routes: Easy, Normal and Hard. However, unlike the original, SF64 only features two versions of Venom, one for the Easy Route and one for the Hard Route, the latter of which is where the Star Fox team has a final rematch with their rivals, Star Wolf.

It turns out the development team had planned on including another variation of Venom for the Normal route, where Fox McCloud would jump out of his Arwing and battle Andross on-foot with a bazooka. According to the staff, this was scrapped due to time constraints. The pilot mode option seen in Star Fox 64's battle mode is actually the repurposed remnants of this idea.

The green planet Peppy's Arwing is shown hurdling towards in the prologue for Star Fox 64 (and also its 3DS remake, Star Fox 64 3D) is actually meant to represent Papetoon, his and also Fox and James' home planet. The Japanese prologue even refers to it as such, and various Japanese SF64 material also mention it. However, when Star Fox 64 was localized for Western audiences, Nintendo of America completely wiped out all specific mention of Papetoon in both the prologue and also manuals/guidebooks.

One of Peppy's most well known lines, "Never give up. Trust your instincts.", was added because Takaya Imamura had requested the game's script writer, Mitsuhiro Takano, to include a stock phrase heard commonly in sci-fi movies. Takano then struggled to play Star Fox 64 as he kept getting hit and failed to make any progress, but as he was thinking of giving it another shot, that line popped into his head.

In the Japanese Versions of the game, after being shot down one of Fox's Teammates will shout out his name, similar to Star Fox Assault, but in the Western Versions, they instead shout "No!!!".

The boss on Solar known as Vulcain, alternatively known as サンガー (Sangā) or Sanger in the Japanese version of Star Fox 64, was originally intended to be the boss for Sector X.

A developer story on the Japanese website for Star Fox 64 reveals Sector X was originally meant to be the "Andross Army Biological Weapon Development Factory", and Fox and his crew were supposed to have engaged with a transport fleet heading for the factory, where they would sneak past the security defenses and enter the interior of the factory, only to find it in a state of disarray due to an accident during an experiment with robots and out-of-control bioweapons attacking all over. They would eventually come across an enemy transport ship attempting to escape only for it to be suddenly destroyed from the inside, revealing Vulcain as the stage's boss.

In the final game, Spyborg (HVC-09 in the Japanese version) is the boss of Sector X, and Vulcain was relocated to planet Solar. Vulcain's beta textures from its tenure as the Sector X boss was recently discovered within files pertaining to Star Fox 64 in the Nintendo Gigaleak.

In the European version, there is an extra language called "Lylat", a made up language which is similar to the gibberish spoken in the original Star Fox.

In the Japanese version, the character icons do not sync with their voices and simply animate the whole way. This was changed in the western versions of the game where the icons would sync with what the characters are saying.

If the player takes too long to defeat the Golemech boss at the end of Venom's easy path (about seven minutes), the fight will end and the player will run into a wall, killing themselves and making the fight restart.

In the Macbeth level, there is a time limit to fighting the boss even if the player missed the Supply Depot ending that leads to Area 6. If the player gets far enough, the boss will state that the player was too slow, and dive bomb the player, killing them instantly. If using a cheat to have infinite health, then the boss will continue to bounce the player upwards until the game crashes.

On the title screen, you can use the analog stick to move the "64" part of the logo around. Fox and his crew will watch it as it moves.

The planet of Katina is a clear reference to the movie "Independence Day". Similar to the movie, you have to dog fight aliens that are invading the world and if you do not finish off the mother ship in time, it will destroy the base with a blue laser. The new partner you get in this fight, Bill Grey, is a reference to the General William Grey from the movie.

The way the characters in the game talk by opening and closing their mouths was inspired by Thunderbirds and other "English puppet dramas" (called "Supermarionation" by Thunderbirds co-creator Gerry Anderson). Shigeru Miyamoto was a fan of these shows and imagined that if the Star Fox series became popular enough, AP Films themselves would come from England to talk about turning it into a "puppet drama".