There are mentions of Subarus deceased dog

In Checkmate, we are told about a cat who was used as archery target practice and burned with lighters. This is not shown on screen though.

Izumi stalks Makoto for pretty much the first half of the original story.

Madara Mikejima gaslights the producer into believing they were childhood friends

Child abuse is part of multiple characters' backstories.

Rinne has a gambling addiction, and Jin has a dependency on alcohol and cigarettes

Mayoi almost added a little "medicine" into their energy drinks but Tatsumi suddenly came (Tatsumi’s 2nd idol story)

There is a brief mention of torture in the prologue of "Tempest", but that's all it is--it's just hypothetical and it's not further discussed.

izumi sena shaved his eyebrows as a kid because he thought that they looked ugly

not really *burried*, but mika once noticed that ritsu didn't move, so he carried him to the es garden and started digging the ground to bury, but the ritsu woke up and said it was some kind of a joke

While more explicit references are limited to the Meteor Impact event story, Kanata Shinkai was raised in a cult which would follow cannibalistic traditions in times of disaster. These traditions are explicitly described within the event story, and directly affect Kanata's life at that point of the story, as well as his morals and self-perception during the whole series. There are also light-hearted gags about cannibalism including Niki Shiina when he is particularly hungry. One particular scene that references Niki Shiina's father's past during the !! Main Story may be seen as having cannibalistic implications, but it's currently just fan speculation.

There are discussions of hypothetical suicide by hanging

In "Checkmate", a character breaks their arm. Another character gives a pretty graphic description of the event in the chapter titled "A Solitary Throne - 7". There's also a more minor example with Tatsumi having broken his leg in the past.

Multiple students are driven to suicide during the hypothetical "War," this is referenced several times in !

One character is constantly kidnapped by another earlier in the story for comedic effect

Kaoru’s mother (mentioned)

Characters speaking of ghosts is not uncommon, however there are no actual ghosts.

Natsume spits on Tsumugi (in Wonder Game i think?)

In Concerto Madara offered Eichi a complimentary drink and threatened to punch it out of him if he ever misbehaves in Leo's show. Another mention of vomitiing was in Shinsengumi in which Eichi was tired ascending to Keito's temple(??) so he vomited.

Eichi Tenshouin is often hospitalized due to terminal illness. There are many instances of hospitals being brought up, or characters visiting hospitals for one reason or another. Instances include the beginning of Checkmate, and Tatsumi Kazehaya's mentions of being hospitalized in the past.

No. Eichi is never said to have cancer and assuming he dose just because he’s terminally ill is extremely abelist

There are quite a few Autistic-coded characters (Nagisa, Sora, Kanata etc). Some of these characters are insulted or bullied for showing autistic traits (strange speech, unusual interests etc)

Both members of Valkyrie are implied/mentioned to have eating disorders. This is talked about more explicitly when Tsumugi asks Mika if he is anorexic.

Leo has been mentioned to struggle with self harm, specifically biting himself.

There are many mentions and threats of suicide. There are two onscreen suicide attempts.

Itsuki is hinted to have it in the anime

Mika Kagehira is shown to have explicit body dysmorphia and talks about it often.

Hinata attempts suicide in Setsubun Festival. Kanata is implied to have attempted suicide by drowning in Meteor Impact. Tsumugi and Shu are shown to have problems with suicide ideation. In the War era, many unnamed students commit suicide, but nothing is shown onscreen

In the older stories, Subaru and Koga referred to Arashi as “Okama”. Okama can either be a term to describe an effeminate man or be the equivalent of the derogatory term used to call homosexuals.

One of the characters is a trans girl and she is often misgendered by other characters

There are a few instances of fatshaming, such as a character being gifted diet pills by a unitmate

There’s a brief hypothetical discussion of incest in Yuta Aoi’s idol story, but no actual incestuous relationships.

There are a few scenes depicting sexual harassment, but nobody is explicitly shown to be sexually assaulted

mayoi is shown to be homeless (lived in basement of an abandoned building) but the building was transformed into a venue for shows

There's fan speculation that the original HiMERU was injured in the same car accident that hospitalized Tatsumi, but it hasn't been confirmed

Tatsumi Kazehaya was previously hospitalized because of a car accident, however the actual scene isn't shown in game

Kanata tries to drown himself in Meteor Impact