Guardroid, the second boss of the game, has a completely different design between the arcade and Genesis versions. The background is also slightly changed between versions, as the curtains in the background are open in the arcade version, showing a couple of moonfish inside an aquarium, whereas in the Genesis version the curtains are closed.

Punisher and Nick Fury's special kick moves (Flaming Sonic Kick and Flaming Flip Kick, respectively) set the enemy on fire in the Japanese version while in the international version these attacks make the enemy bleed.

Both playable characters have a flying fire kick move that can only be done in the Japanese version. It is unknown why this attack was removed from the international version of the game.

Due to the Genesis' inferior hardware compared to the CPS1 arcade board, many of the destructible items in the background are now indestructible. Additionally many NPCs are missing, such as the white dog in the first level.

Bone Crusher, the third boss of the game, has three attacks, one where he uses his flamethrower, one where he launches multiple missiles, and another where he rushes into the player. The flamethrower attack has been removed from the Genesis version.

There's a short cutscene that plays after the player defeats Scully, the first boss of the game, where Punisher interrogates Scully to find out about Kingpin's location, and once he's done he disposes of Scully. In the Arcade version Punisher kills Scully, while in the Genesis version he just tosses him to the side.

Nick Fury smokes a cigarette in the arcade version, with the cigarette being part of his character select portrait and his in-game sprites. In the Genesis version, he doesn't smoke, with the cigarette being completely removed.

The game's final boss Kingpin smokes a cigarette before the final battle. In the Genesis version he doesn't smoke.

The female ninjas' outfit shows more skin in the arcade version, whereas in the Genesis version they are covered up.

According to former Capcom artist Katsuya Akitomo, the game's final boss Kingpin was originally so big he filled half the screen. This was shot down by Capcom who said that "he's a regular human, he can't be that big", and so he was made smaller.

When the game's general planner and visual designer Akira "Akiman" Nishitani told Katsuya Akitomo about this, he pointed out that there have been times where the Kingpin has been drawn as an incredibly large figure in the comics, citing examples such as 1986's Daredevil: Love & War. This bummed Akira Nishitani out.

A PlayStation port for the game was in development by Crystal Dynamics, but it was never completed.

The barrel breaking bonus stage bares a strong resemblance to Street Fighter II's barrel breaking bonus stage. This is most likely an intentional reference since both games were made by Capcom.