Touhou Kinjoukyou: Fossilized Wonders deviates from prior games in the series in that some of its backgrounds were produced with generative artificial intelligence rather than manipulated stock images. This drew criticism from fans who believed that it went against the series' roots in doujin circles, which emphasized DIY approaches from independent creators. Some Japanese fans also accused series creator ZUN of false advertising, due to the fact that the use of generative AI was disclosed on the game's Steam page but not on its DLsite page, resulting in a "Partial AI Use" tag being added there.

ZUN issued a statement during a livestream claiming that his use of generative AI was not meant to be an endorsement of the technology, of which he had a strongly negative view, but rather as an attempt at combating it by "reduc[ing] it to nothing more than a tool." He elaborated that he felt that "entrusting the act of creation entirely to AI means losing to it. However, denying AI outright or rejecting it just because you dislike it is also a form of losing to AI." Consequently, he claimed that "using it this way was my way of asserting that I won't lose when it comes to creative work." ZUN also clarified that the backgrounds were generated using Adobe Firefly, which is trained on Adobe's own stock library and did not draw from unauthorized copyrighted material or independent artists' portfolios as training data.