During the sequence where Aoba uses Scrap on Mizuki, letters start start to pour out of Aoba's body and appear in front of him. This freaks him out and he runs off. The letters were probably going to form a word puzzle like in Koujaku's Scrap sequence, but Aoba didn't know what he was supposed to be doing. Consequently, the player never gets a chance to solve the puzzle, and Aoba inevitably fails to save Mizuki.
When Aoba runs away from the letters, you hear the same laughter that happens when you make a mistake during Mink's Scrap sequence, although this might just be the other people in the room.
During the Rhyme fight at the end of Ren's route, the reason why only Noiz's Allmate was there is because Noiz was the only one to recognize the bug and remove it from his Allmate; all the others would've been berserk.
The 'Murder' part of the title seems nonsensical at first, as there are no actual murders performed (save for some of the characters' flashbacks, and Mink's murder of Toue at the end of his route) but it actually makes sense when you realize that Toue's plan consists of brainwashing people to no end. Notice how the Morphine members looked. They have been endlessly brainwashed to the point that they are considered brain-dead. And if you are brain-dead, you wouldn't live like how humans live normally. In a sense, Toue's plans really is a dramatical murder.
Mink revealed in RE:Connect that the reason why his eye color was different in the first game was because at that time, he was wearing a special pair of contacts that combated the brainwashing lights that were present in Platinum Jail, which would then render him immune to its effects. This meta post that explains why that specific color note His real eye color is gold, but the color of the contacts is blue-green. was used is a very subtle but well-done example of Fridge Brilliance.
In Clear's route, one time Aoba woke up, he realized Clear was watching him sleep, and somehow seemed relieved when he woke up. Then later on, Clear reveals that his grandfather died in his slumber. Therefore the reason why he watched Aoba sleep is because he feared that the same might happen to Aoba.
Why is the only time Aoba bothers to use that stun gun is during Ren's route?
We've seen how Mink and Koujaku's groups can get into Platinum Jail during their respective routes, so how come no one but your chosen love interest ever bothers to come in (barring Ren's route, of course), even though it's completely possible?
In almost all of the bad endings, Aoba winds up either dead or tortured, so why doesn't his evil side come out during them? Especially in Virus' and Trip's routes.
Could also be Fridge Horror when you realize his fate could've been so horrifying that even Desire wanted nothing to do with it.
that explains why that specific color note was used is a very subtle but well-done example of Fridge Brilliance.