In June 2023, a patch was released that altered and censored elements deemed insensitive and exploitative by Hidden Variable Studios, Future Club, and Autumn Games. This update was widely negatively received by fans and resulted in a review bomb on Steam lasting several days, gradually causing the Recent Reviews quality marker to dip into "Overwhelmingly Negative" until all reviews since the update's release were eventually frozen from the game's overall reception by Steam in response. Many of the fan reviews called the changes both a form of censorship and removal of paid content, and included, but are not limited to:

• The removal of in-universe allusions to real world hate groups and upskirt shots of teenage fighters.
• Toning down depictions of racial violence and other sexually suggestive content in the story.
• Deleting or altering several illustrations from the guest art gallery.
• The removal of several voice lines, most notably the Real Soviet Announcer voice pack due to previous allegations and ongoing lawsuits between Future Club and Mike Zaimont, the pack's voice actor and Skullgirls' former lead designer/programmer. This voice pack's removal especially drew criticism for previously being promoted as a $700,000 stretch goal during the 2013 "Keep Skullgirls Growing" Indiegogo campaign.

Current game director Charley Price stated that the updates were made in order to "reflect the values and broad vision for Skullgirls moving forward".

On April 23rd, 2015, an update was released that altered some frames of animation for Filia, Fukua, and Cerebella. This was done with the purpose of removing or heavily obscuring some panty shots, as the developers considered them to be unnecesary fanservice.

Additionally, two unused animations for Filia were also removed from the Digital Art Compendium. These animations include a time over animation where Samson tears apart the top of her shirt while she tries to cover herself up, and a taunt where Samson spanks Filia hard enough to make her fly a short distance and land on her knees.

On May 23, 2022, it was announced that Valentine was receiving another design update that would incorporate pink shurikens that replaces the original cross. Not only will this affect Valentine's original sprite animations for both the console/PC and mobile versions of the game, but also any story mode art as well as other art pieces included in the Digital Art Compendium.

Valentine's design was officially changed on May 13th, 2014 via a patch update. The update changed all parts of her design that involve a red cross against a white background to be altered so the cross is colored pink instead. This was done in order to prevent legal action by the International Committee of the Red Cross.