The series sometimes thrives on this, as noted below:
I: Mote's whole dreamworld stitch, and Myria's portrayal in The Dragon Warrior manga adaptation.
II: The opening where you go from beloved resident of Gate to no one having any recollection of you (shudder). Most of what Habaruku does. The worst ending. The final dungeon's pulsating-flesh appearance.
III: With a bit of Fan Disservice, Myria's One-Winged Angel, especially when she uses her physical attack (guts literally busting out) and her special attack Holocaust, which involves her face melting off. Graphically.
IV: Elina's fate. The Carronade and anything to do with how it works and what it does. Ryu's breakdown, who even terrifies Nina, who had never shown fear of being that close to a dragon before. The Fou Empire's predecessors, with their three attempts at summoning caused the first to spawn with only a head, the second to spawn with no physical body, and the third to be split in half and spread across 600 years.
The manga adaptation seriously drives this point home with both the Carronade and Ryu's breakdown: The former with Mami, who is tortured with hot irons and who is explicitly described as having suffered every torture the Empire could throw at her and the latter Not only showing the Kaiser Dragon on a Godzilla-esque rampage (complete with depictions of Fou Empire solders being torn asunder), but it's shown that Kaiser Breath is capable of boring holes in mountains.
DQ: The room full of headless Ninas in People Jars. Bosch and his demonic-looking arm (the monstrous features even reaches up to his face). The Non-Standard Game Over.
Nina. In addition to having been turned into a human HEPA filter, her tongue was cut out to boot—so she couldn't tell people what happened.
Bosch (1/64), after he has bits of Chetyre grafted onto him.
Everything about what Yuna does to sacrifices for the Carronade qualifies. In order to make them potent offerings, he tortures them in the most painful ways imaginable into their minds completely break.
It gets particularly terrifying when the party explores his laboratory at the end of the game. The music becomes unsettling and sounds like something out of Silent Hill. A thick mist fills the entire building, and at the end the party comes across masses of organs in flesh that they must climb to reach the top of the structure. One particularly creepy instance is when they reach a room with a bloody white cot and a diagram of the human body next to it. When they finally reach Elina, he reveals that he transformed her into an immortal Endless that he plans on using as an eternal battery for the Carronade.
The manga's depiction of this scene is quite possibly even more disturbing. In one scene, Ryu slices through what look like a mass of giant intestines, and in addition to the above, Yuna also describes graphically how he created the Dragonslayer—by summoning only the head of an oni-like god, studying and torturing it, and then fusing its spirit into the sword. And yes, the manga shows how only the head came through with the god in question essentially doing an I Have No Mouth and I Must Scream.