When completing Arcade Mode as Bridget, one possible ending depicts her coming out as a transgender girl, having previously been depicted in earlier games as a cisgender boy who was raised as a girl. This plot development attracted rumors that it was a "bad ending" exclusive to the English localization and that Bridget was still a crossdressing boy in the Japanese release. Eventually, director Akira Katano and developer Daisuke Ishiwatari confirmed on their "Developer's Backyard" blog that Bridget was indeed intended to be a trans girl in the Japanese version and that the game's endings were not written under the pretense of them being "good" or "bad," stating that they simply showcase different, coexisting aspects of each character, indicating that Bridget's trans identity is in place across both of her Arcade Mode endings.

On the game's Digital Figure mode, there's a picture of the 42nd President of the United States Bill Clinton. It can be found on the "White House - Oval Office" environment. The picture can also be found in the background on the game's story mode.

This is a reference to a 1999 presidential speech speech condemning video game violence, where Clinton held up an ad for the original Guilty Gear with the tagline "Kill Your Friends Guilt free".