Parasoul's original wakeup animation (featured in the original 2012 Xbox Live Arcade/PlayStation Network release) showed the character's buttocks and underwear as she stood up from the ground. This was changed in the 2013 PC release, with her dress being longer and thus removing the partial nudity.

According to former lead design director Mike Zaimont, "Her skirt was actually the wrong length in the original version, it was fixed because it was off-model."

On April 23, 2015, designer Earl "earlfriend" Gertwagen made a statement on the official Skullheart forums explaining that the reason why the game isn't available on either the Nintendo 3DS or the Wii U is because Skullgirls cannot run on the former and the lack of a publisher for the latter.

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".

Finishing the match with any Blockbuster attack will cause the background to change and display a portrait of the defeated character with a pained expression on their face. This is a reference to the Capcom fighting game JoJo's Bizarre Adventure, which features similar portraits for when a match is finished with a Super. The shaders that Skullgirls uses for its portraits in-game are also internally labeled as "JojosDeathPortrait" in the game's files.