At the very start of the game, the scene fades out from Hajime being awoken by Nagito to a command line interface that ends with the words "GAME START". This is soon followed by Hajime's text glitching and him standing before a classroom door within an empty void. This doesn't come back into play again until the last trial, when it's revealed that the entire school trip was in fact a virtual reality.
In the hidden scene in Chapter 1 of the girls cooking, Chiaki invited Monomi despite most of the students disliking her, and feeds her some of the desserts she made in the same scene, hinting at their connection. She's also the one who gets Monomi to keep Monokuma from entering the old lodge during the party. Additionally, Chiaki is the only one of the students that respects Monomi, whereas everyone else tells her off or verbally abuses her because they believe that she's an accomplice of Monokuma who is only pretending to oppose him. Also, while Sonia never once insults Monomi or is rude to her, she clearly doesn't trust her, unlike Chiaki.
Right before Monokuma shows up, Hajime gets nervous and has a feeling that everything's going to go horribly wrong. He probably subconsciously remembers that he, as Izuru, made sure that something was going to go wrong by uploading Alter Ego Junko.
After the culprit of Chapter 1 is executed and before Monokuma uses Exact Words to go back on his promise to restore everyone's memories, Monomi acknowledges that everyone has indeed had their memories taken away from them, and she also implies that restoring their memories would be really bad.
On Peko's report card, her "like" is listed as the color black, hinting at her secret attraction to Fuyuhiko.
Early on, Monokuma announces that there is a "traitor" in the group of sixteen students. In many official images, such as the soundtrack album or even the image at the top of this page, Chiaki Nanami is either drawn separately from the main group or in a markedly different way (such as being upside down). She's the one who doesn't belong in the group.
This becomes particularly evident at the start of the fifth trial, when the students' portraits are shown. They're divided into three pictures, and they're blue if alive and red if dead; at that point, Chiaki is the only blue one in her picture.
Additionally, some of the decorated backgrounds behind the characters in the game's intro tell of later events. For example, Gundham's background is that of glowing "magic circles", and during his execution he tries to save himself by drawing magic protection circles on the ground.
On the topic of Gundham, his first Free Time event has him ask Hajime his "True Name". While it is a question asked due to Gundham's eccentric behavior, it seems more ominous given the reveal of Izuru Kamukura.
When Mikan has Hajime check up on Nagito in the Hospital near the end of Chapter 3's Daily Life, trying to enter Akane's hospital room causes Mikan to tell Hajime that they should check on Nagito first. However, checking Ibuki's bedroom causes Mikan to tell Hajime not to disturb her because she assumes she must be asleep due to the Morning Announcement not having played yet, and she adds that she is not 100% sure of this, but that they shouldn't bother her anyways. It makes sense that Mikan would get nervous about Hajime checking Ibuki's bedroom but not Akane's, since Mikan had lured Ibuki to the Music Venue and killed her earlier during the night, so Hajime would definitely get worried if he noticed that Ibuki was missing before Mikan could put her plan into action.
Another case happens with "The Wizard of Monomi", which was used as a basis for a "copycat murder" in Chapter 3. There were three deaths in the movie but only two murders in that chapter, because the most people a culprit can murder is two. The third unused death was "Tin Monomi being broken down into a heap of scraps." Guess what happens to Mechamaru the next chapter. For added irony, the person who points this out is the one who kills him.
Monokuma establishes with the students at the beginning of Chapter 4 that, even though Nekomaru has become Mechamaru, killing him will still count as murder, but notes that there's also the possibility that Nekomaru will kill another student himself, which the latter insists will never happen. He becomes the victim of the chapter, and it is indeed counted as a murder. Furthermore, since he was fighting Gundham to the death as part of their pact, if Nekomaru had won the fight instead (a very real possibility), he would have ended up becoming a killer.
During chapter 5 before one of the breakfasts, if you talk to Chiaki she will say that she had dreamed about a game involving Monokuma blocks that she couldn't win. Guess what happens to her after Class Trial.
The interface indulges even more in retro 8-bit aesthetics than the previous game, which hints at the events of the story being a literal game inside of a computer program. The prologue has some Ominous Visual Glitches which return at the end of Chapter 5, and the title sequence is that of a retro computer program startup sequence. This helped by the music suddenly turning into a chiptune version of the final investigation theme in Chapter 6 as the simulation continues to break down.
When Monokuma usurps Usami and turns her into Monomi, the latter notes with horror that even the UI now lists her name as Monomi. Rather than a light-hearted fourth wall breaking, this is yet another evidence of Monokuma having seized utter control of the simulation.
Red and black were the two colors Nintendo's [first] VR headset, the Nintendo Virtual Boy, rendered graphics in. Those two colors so happen to be the palette of choice for the pre-execution animations, which hints at VR being involved to whoever canny enough to make the connection.
Besides having gained a few pounds, Byakuya is a completely different person compared to the first game. Where in the first game he watched everything play out with an almost perverted sense of glee, here he immediately proclaims he won't let anybody become a victim. On the side, when it comes to gift-giving he now loves the junk food he previously rejected and hates one of his favorite presents from the previous game (Kopi Luwak/"civet coffee"). Come chapter 5 and it all makes sense.
Along with this, his Monokuma File is the only one to not list a name in the Truth Bullet section of the handbook. It only lists "The victim's body."
While exploring the library at the beginning of Chapter 2, Peko is visibly unsettled by Sonia's admiration of serial killers. Her later claim to be one of them, a self-righteous Knight Templar, turns out to be false.
Monokuma also often directly makes references to them being in a virtual world pretty often typically in the form of Exact Words while being a Troll. Most obvious cases are insisting on addressing things with game terminology and the Stealth Pun he makes when telling them about how the Despair Disease spreads. To clarify: He tells you they are caused by invisible bugs. Upon The Reveal that everyone is an avatar and all their real bodies are in pods that make physical infections impossible, it's obvious he is talking about computer bugs that are causing these symptoms by messing with the avatar's data directly, causing massive behavioral shifts and unlocking previously inaccessible memories in the case of Mikan through the glitches they are causing.
When protecting Akane from a bazooka blast, Nekomaru manages to hang on long enough to be turned into a robot. Why wasn't he blown into pieces? Because he's in a game!
During chapter 4, Nagito intentionally makes a game of Russian Roulette more difficult for himself by loading up five bullets instead of one. This is similar to his "assisted" suicide in chapter 5, where he crafts a murder that is impossible to solve, meaning the culprit—one student out of six—must be picked randomly.
Mikan's unhinged, creepy behavior once she's exposed as the murderer in Chapter 3 makes a lot more sense once you reach the final trial and learn that the whole group were the Despair Remnants, and that the "beloved" she was referring to was actually Junko. Her cryptic quotes and repeated cries of "Forgive me!" also make sense after learning she and the other Remnants brought forth the Tragedy and the Jabberwock Island simulation was their chance at redemption.
When Hajime wakes up with Mikan on top of him the second time, he mentions that she feels hot. It's later revealed that she was infected with the Despair Disease (which always comes with a fever), and after the trial, he laments that he didn't pick up on that earlier.
Up until his execution, Teruteru repeatedly says that everything happening isn't real. He may be fully in denial, but as it turns out, he's actually right—they're in a virtual world.
A subtle hint at Nagito being his own killer (even if it was through other person's hands) is given since the very beginning of the trial. Victims get rather similar-looking crosses over their portraits while perpetrators get distinctly customized ones (a first aid symbol for Mikan, a fork and a knife for Teruteru, etc.), and Nagito's cross is dripping blood.
In Chiaki's final Free Time event, she states that she wants to learn more from Hajime with a big smile. Hajime retorts that he'll be happy to once they leave the island, at which point her smile fades and she asks Hajime not to forget about her. Because she's an AI, she naturally can't leave the island.
While investigating the final island for the first time, a background detail in the robot factory shows what appears to be a humanlike-robot in the middle of being assembled. While it's never finished, this is the same island where Chiaki is charged with being "the murderer", and she's really an AI.
During the investigation of Strawberry/Grape Tower on the fourth island, Chiaki gets an idea and puts her E-handbook on the floor to see if it'll appear in the other tower if her suspicions of both towers actually being the same building are correct, which gets confirmed when it appears on the other side. An astute player may notice that it's exactly the same orientation from when she placed it rather than it logically being rotated 180 degrees, hinting that the tower is actually a giant elevator, a crucial piece of evidence in the coming case.
