In the cinematic that plays after defeating now former Star Wolf member Andrew Oikonny, a strange aparoid appears firing a beam at one of the characters. In the Japanese version it's done to Slippy, whilst in the Western versions it's done to Krystal.

Some lines in the opening prologue stage for Star Fox: Assault contain allusions towards dialogue from Area 6, one of Star Fox 64's final stages. In the latter, Caiman says near the end that "The last line has been breached!", and the Area 6 commander will respond with "These guys are crazy!". In the Japanese version of Star Fox 64, the latter instead says "こいつら、化け物か！" (These guys are monsters!)

In Star Fox: Assault's prologue, one of the ape soldiers apart of Oikonny's rebellion will similarly shout that "Our final line of defense has been penetrated!". Oikonny in response says "Is this guy some kind of demon?". In the Japanese version of Assault, he instead says "コイツら化け物か？" (Are these monsters?), which makes it much more clear that it's meant to be a callback to Area 6's dialogue. This intention was confirmed by producer Takaya Imamura in a 2005 Nintendo Dream interview with Star Fox: Assault's development team.

Star Fox: Assault is notable for including three unlockable Famicom/NES games originally created by Namco:

• Xevious
• Battle City
• Star Luster

As explained by the development team in an issue of Nintendo Dream, this was done to highlight Star Fox: Assault being a collaboration between Nintendo and Namco, with the latter being its primary developer. With the Star Fox franchise being a sci-fi shooter series, Tsuyoshi Kobayashi and Takaya Imamura had carefully decided on which classic Namco games would fit the best with that vibe. There were considerations to also include Nintendo created Famicom/NES games (one person, for example, had suggested including Balloon Fight), but ultimately Imamura and Kobayashi couldn't come up with any games that would have fit the Star Fox world and atmosphere.

Unfortunately, as the Famicom versions of Battle City and Star Luster had never been released in Western territories, they in turn were excluded from all Western versions of Star Fox: Assault, leaving Xevious as the only unlockable Namco game outside of Japan.

The subtitle of Star Fox: Assault was suggested by Nintendo of America. Initially, there were legal concerns as Namco had already trademarked the name "Assault" for their 1988 arcade game of the same name. Fortunately for Nintendo, the trademark was only valid within Japan, and Namco, who were already the developers for Star Fox: Assault, had granted them permission to use the title.