There is a moment where one of the main characters (who has just gotten out of prison) stares at a girl and spends an uncomfortable amount of time hovering over her after accidentally knocking her to the ground. Nothing actually happens, but the scene is worth warning about.
While there is no rape at all in the game, there is a slight mention of it in the original release. It has been relocalized as "delicate flower" in the remastered version.
There is an uncomfortable scene where a man who has recently left prison is on top of an underage girl and staring intently at her. Nothing comes of this. It is implied he was looking at her sexually. This is not specifically because she is a minor, but because he has not so much as seen a woman in many many years.
The first part of the game (Akiyama's section) has a major plot point involving a venue which is consistently referred to as a "[t-slur] bar" in the English translation. This was altered in the remaster to remove the use of slurs (including having the spoken Japanese dialogue rewritten and re-recorded), but the plot remains overall unchanged.
It is implied Haruka suffers some form of PTSD following watching Kiryu being stabbed at the end of Yakuza 3. When the perpetrator appears in this game, Haruka freaks out.
There is a flashback cutscene where one of the main characters are chained to a structure and his eye is gouged out. It isn't explicitly shown, as the attacker hides the actual removal with his body in the camera shot, but there is audio.
One of the side characters, Hana, is the subject to a few jokes in reference to her weight, explicitly or otherwise. She is then subject to the trope at the end of the game where she loses weight as a form of development.