In 2024, Ubisoft faced controversy over two instances related to the game's marketing prior to its release being delayed. The first instance revolved around them using a flag created by the Sekigahara Teppo-tai, a Japanese historical re-enactment group, as part of the game's concept art and marketing materials without the group's permission. Ubisoft Japan would later issue an apology for this, agreeing to remove the flag from the game's website, but stated that it would likely remain in the concept art as part of the game's printed art book, something that the Sekigahara Teppo-tai would later request be removed as well. On July 23, Ubisoft posted an apology to Twitter for including material in their marketing that "caused concern within the Japanese community".

Two months after this statement, Ubisoft would face criticism again for a collectible figurine produced by PureArts featuring the protagonists Yasuke and Naoe standing in the ruins of a one-legged torii gate. This drew ire from critics who were already upset over Ubisoft's handling of the game's historical background, as the only known one-legged torii in Japan is located at the Sannō Shrine in Nagasaki. This torii was one of the few surviving structures after the United States' atomic bombing of the city in 1945. It became one-legged as a result of it being within 900 meters of the explosion's hypocenter, and serves as a local reminder of the bombing today. On September 24, just a few days after the figurine's announcement, Ubisoft cancelled their appearance at Tokyo Game Show for "various circumstances" (likely including these prior marketing controversies among other development factors) and later announced that the game's release would be delayed into the next year to allow for more time to polish it. PureArts' pre-order page for the figurine was removed from their website around the same time. They later released a statement on October 15 apologizing for the "insensitive design" and stated they would redesign the figurine for a later release.

When it was announced that Jonathan Dumont was working on the game, many Ubisoft Quebec employees reportedly refused to work with him (with some even outright quitting) due to past allegations involving abuse and sexual misconduct. In response, Ubisoft CEO Yves Guillemot stated that they take all allegations "extremely seriously", and that Dumont had been "appropriately disciplined" and cleared to continue working.

Yasuke is the series' first main protagonist to be based on a real historical figure, but his real-life identity and status serving under Japanese daimyo Oda Nobunaga has been the subject of a contentious debate among historians. There are few scholarly/historical resources available describing him and his life, and no known resources from when he was alive that refer to him as a samurai, with the most common belief being his title was a retainer.

His reveal as a lead in the game on May 15, 2024 caused polarizing reactions worldwide on social media. Fans critical of the decision claimed Ubisoft were going against the series' penchant for accurate historical backgrounds and misrepresented Japan, which the series had never covered in-depth, by inflating Yasuke's role in history and not having both protagonists be Japanese (the other protagonist, Naoe, is Japanese), claiming he was not actually a samurai. Fans in support of his role claiming he was actually a samurai called these objections racist and based on narrow-minded arguments and inferences, with some claiming that Asian samurai protagonists in media were oversaturated and that complaints would be the same if the game was set in Africa and starred an African protagonist. This intense fighting led to an edit war on Yasuke's English Wikipedia article, with administrators publicly calling its Talk page "a complete dumpster fire". As of October 8, the consensus that the Talk page reached appears to be that the available historical resources are inconclusive as to if he was or was not a samurai, but that scholars consistently describe Yasuke as a samurai without any sources found where scholars do not describe him as one.

This speculation and debate allows popular media to take creative liberties in adapting him, often depicting him as a high-ranking samurai, and Ubisoft seemed to take a similar direction from the outset. A press release at the game's announcement stated:


Despite the header used, the quote is carefully worded to stop short of directly calling Yasuke a samurai, with more advertising describing him as a "samurai of historical legend". Game director Charles Benoit later acknowledged his life "is surrounded by mysteries" and that "[Yasuke] told us to tell" his story seen in the game, which was also described by associate narrative director Brooke Davies as historical fiction.

Creative director Jonathan Dumont stated in a Famitsu interview on May 15 that they chose Yasuke to fit with the story of a foreigner who fights off oppressing forces like the Portuguese slave trade, while exploring a country unknown to him alongside the player, stating that they were "first looking for "our samurai," someone who could be our non-Japanese eyes". The following day, the interviews were edited to remove this quote, and to change quotes either directly or contextually referring to Yasuke as an "outsider" to being a "foreign-born samurai". After further mounting controversy, Ubisoft posted a statement to Twitter in English and Japanese on July 23 apologizing for elements in their promotional materials that "caused concern within the Japanese community", reiterating that the game's story was intended to be historical fiction and not an accurate recreation of events, and that Yasuke's real-life status was "a matter of debate and discussion". The Japanese statement received Community Notes pointing out their stance contradicted several quotes from both Famitsu and an Xbox Wire interview that emphasized confirming historical accuracy, but was removed from the statement hours later.