A dog is implied to die in a late sequence where it's owner is hit by a car. It gets thrown in the air in the chaos and the scene changes before we see what happens to the dog.
In Episode 28 of the anime and Chapter 118 of the manga, a young boy with a bullet wound is rushed into hospital - it is revealed that his father shot him.
Sort of. In Episode 6 of the anime and Chapter 23 of the manga, Thunder McQueen attempts to drown himself. His Stand reflects this onto Ermes, by making a 'bubble' full of liquid around her mouth and starting to drown her. She gets away from this.
All of the major characters die besides Emporio - though most of them turn up as slightly different people in an alternate universe after Pucci is killed.
Pucci, Weather and Perla all die - they are each other's siblings. Donatello, brother of Rikiel and Ungalo, also dies - the other two brothers' fates are unknown, but it wouldn't be unreasonable to assume that they both died as well.
Jolyne is arrested at the beginning and is put into Green Dolphin Street prison. The first two-thirds of the story revolve around Jolyne being in prison, until she and her friends eventually break out.
Foo Fighters, who is a colony of plankton granted intelligence via a Stand disc and possessing a woman's corpse, dies in Episode 22 of the anime and Chapter 95 of the manga.
In the beginning parts of the story up to the Foo Fighters arc, one of the prison guards carries an alligator puppet called Charlotte.
In Episodes 13 and 14 of the anime and Chapters 53 and 54 of the manga, an invisible zombie is made from the corpse of a stuffed alligator. This alligator attacks Jolyne and friends, but is soon killed.
In Episode 33 of the anime and Chapter 138 of the manga, Ermes and Jolyne antagonize some alligators at the side of the road and toss a ring at them, though none of them pursue the protagonists.
I don't know what other category to put this in but nobody's mentioned it - a main ally Annasui is in prison because he murdered his ex-girlfriend for cheating on him. He's infatuated with the main character and exhibits tons of red flags like being pushy with his advances, getting angry when she shows affection to her friends and deciding that he's going to marry her without even telling her. He may make you uncomfortable throughout the part
One of the villains has the ability to prevent people from forming new long term memories. She goes out of her way to destroy notes that characters are writing about things they need to remember. The entire sequence lasts for around 2 episodes before the characters she's doing it to manage to break the effect and is rather disturbing.
In Episode 2 of the anime and Chapter 5 of the manga, Gwess seems to get angry at a pet bird and threaten to deprive it of food whilst roughly squeezing it in her hand - the bird turns out to be a human she's shrunk and stuffed into the corpse of a bird, but it may be upsetting to see before knowing this.
In Episode 31 of the anime and Chapter 128 of the manga, Perla is restrained and almost forced to kiss the racists who attacked her and Weather. She is only 14.
A couple of scenes with Ermes that look like they may turn into this- first when she is physically assaulted by two guards in a prison bus near the start (they are interrupted). Second, while she is asleep in the infirmiry a janitor caresses her leg (to steal money she has strapped to it). However there is a more explicit threat of this to another character later during Weather/Pucci's backstories when a group of men restrain a teenage girl.
A character has the ability to view the earth's memories by literally digging them up. If he digs up the memory of a person it tends to look like he's digging up a living human even though its only a memory.
The backstory of a character mentions how shortly after they were born, they were swapped at the hospital with a baby who was born and died on the same day.
Sports Maximum has the ability to revive the dead as mindless zombie ghosts and ends up becoming one himself with his personality still largely intact.
Up to when the protagonists escape prison, there are swamps. In the Heavy Weather arc, a lake is featured in Pucci's backstory. In the Made In Heaven arc, the protagonists fight Pucci in the ocean.
Foo Fighters is a sentient colony of plankton that becomes one of the heroes after being fought. They avoid suspicion by possessing the corpse of a dead prisoner.
A child pees his pants, and his urine is shown to be bloody. There's another scene where two main characters pee in an anti-gravity environment and you can see the pee floating, and another character mentions drinking their own pee.
There is a fight scene that takes place involving an electric chair (Dragon's Dream), and a character attempts to kill himself through electrocution (Highway To Hell).
In the Highway to Hell arc, Thunder McQueen repeatedly attempts suicide. In the Heavy Weather arc, Wes repeatedly attempts to kill himself after learning of Perla's death, but is saved each time by his Stand's abilities.
One character initially has a very feminine appearance and then later on another character is surprised to learn they are a man, though they don't make any jokes about it
The main characters are technically homeless after they escape from prison, but it's not touched upon. Emporio becomes homeless after the final battle, but it isn't addressed and the ending implies he'll have a place to stay.
Tehcnically; An antagonist has a power to make accidents (that have caused casualities)"happen again" They use their power to trap the protagonist into projection of a plane that crashed years ago; and is destined to crash again the same way.
Yes, very much, including the following:
Sniped, lit on fire, hanged, shot with shotgun while commiting suicide by jumping off a building, hand turned inside out, committing suicide and failing 3 more times, big fight to the death with multiple people, body dissolving with no trace, and ribcage as a trap. Plus way, way more