The SNES version of the Ruins (Chao's stage) has the ship and power lines removed for unknown reasons.

There was a planned boss for the Graveyard named Necrosan, but the idea was scrapped.

Due to the lack of a backflip animation, Talon does a frontflip even while jumping backwards.

The Primal Rage design team implemented an unusual and largely unknown security method into the arcade machine's coding that prevented the full features of the game from becoming active when emulated. Since the original programming team has since moved on to other things, they could not be reached for questioning regarding the game's security lock-outs. Those who have been contacted expressed no interest in unlocking the ROM BIOS for freeware distribution or security corrections. For these reasons, no perfect emulation of the original arcade game exists.

In the absence of these security protections, blood would be "censored" in that it would be colored a yellowish color with a brown shading. Also, fatalities could not be performed, and many special moves were not available. Another emulation problem was the player could no longer chain attacks, which greatly decreased the chance of performing a combo. These issues even affect the Midway Arcade Treasures 2 collection, which would supposedly feature an arcade perfect rendition of the game, but instead provides a censored and incomplete version.

A mother from Gilber, AZ started a grass-roots campaign in 1996 (2 years after the game's initial release) that resulted in the game being pulled from various stores nationwide. The controversy started when her 11-year old son executed Chaos' "Golden Shower" fatality in which Chaos finishes his opponent off by urinating on them.

Time Warner Interactive, the publisher of the game, dismissed the claim because the mother went straight to the media and not to them or the developer Atari. They proved their point when they re-submitted the game to the ESRB board for another rating, but the board stuck to it's original "T" (Teen) rating and called the mother out for letting her 11-year old play a game that rated above his age.