According to Street Fighter 6 director Takayuki Nakayama, Captain Commando is set in the future of the Street Fighter universe. This has been hinted at via numerous references to another series set in the same universe, Final Fight. Specific examples of this include Captain Commando taking place in Metro City (a recurring location from both Final Fight and Street Fighter) and Ginzu being trained in the fictional Bushinryu Ninjutsu style of fighting used by Guy. Nakayama at one point revealed that Ginzu's father Gou (a character who had previously only appeared in concept art) would eventually succeed Guy as the 40th Bushinryu Grandmaster, with Ginzu eventually becoming the 41st Grandmaster.

Gou would later make his official debut in Street Fighter 6's World Tour mode during Kimberly's second memory dialogue, where she mentions how she was easily beaten by him. His appearance here depicts him wearing a purple version of Guy's Bushinryu outfit (similar to Ginzu's uniform) and holding a katana similar to Ginzu's signature weapon Lightning Light. Another reference in World Tour mode comes in the form of Carol, one of the minor enemies from Captain Commando appearing as an opponent during the "Fighty Mighty" mission quest. Her appearance is loosely based on her in-game sprite, wearing a blue tank top and pants as well as having pink hair (though here it's depicted as being straight rather than a ponytail), and her dialogue upon being beaten alludes to her role as a criminal in the original game: "Reminds me of old times, back when I was involved in some...slightly unscrupulous business."

There is one known continuity error with the game being set in the Street Fighter universe. In the Character Reference section of the Street Fighter V Shadaloo Combat Research Institute website, the profile for Yuta Homura mentions that he can clear Captain Commando using Mack the Knife (under his Japanese name Jenetty, "ジェネティー") with a single credit. The game is not mentioned by name though, and is instead referred to as an unspecified "beat'em up action game".

Ginzu and Mack the Knife were censored in the SNES version of the game. In the arcade version, if most enemies receive a lethal hit from Ginzu or Mack, they can be dissected or will melt away respectively. As such, Ginzu's profile in the arcade version mentions that he is capable of dissecting his enemies, while Mack's says he can melt them. All of these details were removed in the SNES version, and most enemies will instead simply drop to the ground when they receive a lethal hit from either of them.

It is often said that Mega Man was once used as Capcom's mascot in the 1980s, in a similar way to how Nintendo and Sega use Mario and Sonic respectively. Like many other statements of platforming characters being used as corporate mascots, this is untrue, as Mega Man has never been used to promote the wider Capcom brand of software outside of his own games or crossovers in which he appears. However, Capcom did have a mascot in the 1980s: the titular hero of Captain Commando - many earlier NES Capcom games were branded as part of the "Captain Commando Challenge Series", including licensed titles such as DuckTales, with game manuals having signed messages "written" by Captain Commando. Despite this, Captain Commando was never released on the NES.

Capcom's former community manager Seth Killian addressed Capcom's current lack of a mascot and Mega Man's use as an unofficial mascot on the Capcom-Unity forums in 2009:

In the arcade version, there are armed enemies which drop fire arms when they die, which can later be used by the player. These enemies along with the usable weapons were removed from the SNES version.

If the player lands a lethal blown with Captain Commando's flamethrower or similar fire attacks the enemy will burn until they turn into ash. This does not happen in the SNES version, where the burned enemies stay on the ground before dissapearing.

Some of the enemies in the game have Ride Armors which the player can also control. This feature wasn't available in the SNES version, with the Ride Armors being completely removed.

The enemy known as Mardia attacks by spitting green slime to the player. Because the attack makes it look like she's vomiting, this was changed in the SNES version where she throws bombs to the player instead.

At the beginning of the level you can see two enemies smoking cigarettes while squatting. This does not happen in the SNES version.

Blood and pink smoke (the latter happens when Mack hits the enemy) were removed from the SNES version.

The outfits of the female enemies Carol and Brenda show more skin in the arcade version, whereas in the SNES version they are more covered up.

Some of the characters have different names across regions.

•The playable characters Sho, Jennety, and Hoover were renamed to Ginzu the Ninja, Mack the Knife, and Baby Head respectively.

•The 7th stage boss Blood was changed to Boots. This change was exclusive to the SNES version.

•The final boss Genocide was changed to Scumocide.