When the MSPA Reader escapes from Doc Scratch's place, the connection to the other side of the fenestrated wall is cut off, similar to what happened to Roxy at one point. If they hadn't discovered the logo, they quite possibly would have been stranded in the Furthest Ring.
Speaking of the logo, the when they touch it, they gain its powers... but they also lose their memories of everything that happened before it. And since John didn't lose his memories when he gained its powers, it's implied that something else caused that to happen.
The Reader accidentally loses John's copy of Sburb. There are loads of consequences that could result from this, especially since the canon of Homestuck relies a lot on Stable Time Loops.
Once again, the Reader has vague memories of the events of Friendsim and the different endings from that game, including their own deaths.
Volume 3 makes it clear how bad Dave's living situation is. He mentions that there are times where he has to stay on guard for any sudden surprises, only for those surprises not to happen, and that he can't use the facilities, having to wash clothes in the shower and keep food and drink in places other than the fridge. It also reminds us that there are cameras around the apartment - one of them comes out of the fridge, and looks straight towards you.
The ending itself - when the Reader decides that Dave isn't safe here, they try to zap him away while the camera is still watching. Before they can, however, Bro shows up and throws them out of the window.
In Volume 4, Jade reveals that since the Reader stopped John from playing Sburb, all copies of the game no longer work, she doesn't dream on Prospit anymore, and the Trolls have stopped contacting her. Which means that the timeline might be turning into, or has already turned into, a doomed one.
If they try to take Jade's gun from her, Bec teleports them into space, leaving them to die from the lack of heat and air.
Jade's second bad ending is much Bloodier and Gorier than the other bad endings in this game so far. If the Reader tries to fight Bec, he bites them and causes them to bleed a lot, with blood covering the screen. They escape through Bec to the Green Sun, but it's made clear that they're dying from blood loss.
Actually, the figure is described as bearing leathery wings with dark tendrils trailing behind. A crow's wings aren't leathery. This, combined with the fact that the prospitians didn't recognize Jade, implies that they somehow ended up on the troll's version of Prospit, especially since MSPA reader found Karkat and Kanaya through this Prospit.
In keeping with Jade's Route discussing the consequences of the MSPA Reader's interference in canon, Dave in Jade's Good Ending Path mentions how he can't come to Jade's because he's not sure if Bro will like that, especially since he was giving off some "rank vibes" after Dave left the house to go to Olive Garden, which already gives off some uncomfortable imagery of abuse, but worse still is how he mentions that when he thinks about it, Bro's vibes have been "off" ever since John's Birthday. Implying that after training Dave since he was a baby for Sburb, only for Sburb to suddenly not happen when it was supposed to, is beginning to have a... not good effect on Bro, which doesn't look good for Dave's home life.
Karkat's route in Volume 5 has quite a bit of this. His first bad ending involves him accidentally killing the MSPA Reader if they zap over to him instead of walking, by attacking them on instinct when they appear. He is shocked at discovering that their blood colour is the same as his, but the Reader dies before he can say more about it.
When the Reader wants to demonstrate their powers, Karkat suggests going to Gamzee's hive, but they end up inside it rather than outside. He panics when Gamzee approaches, and they zap away again, with him gripping the Reader so hard that they start to bleed. Just what was it exactly that made him so terrified all of a sudden? Gamzee's dialogue also suggests that someone else is there...
When a drone comes to the neighbourhood, Karkat takes them into a hole in the floor and panics again, saying this is something he often has to do. The background music even changes to something more suspenseful, and whirring sound effects can be heard.
If the Reader follows his instructions to stay, the drone discovers them, which results in Karkat being found out by the drones as someone who must be culled, and his hive being burned down from his lusus' attempt to save him, which also kills him. The Reader keeps zapping all over Alternia with him to escape from the drones that are now after him, only for them to keep showing up. Worse still, he blames the Reader for this and leaves them, and it's likely he won't survive for much longer if the whirring that plays during the ending card is anything to go by.
Volume 6 reveals what was happening in Gamzee's hive in the previous volume - it was the future version of the MSPA Reader who he was talking to. They realise they've travelled back in time when they hear noises coming from the closet, and if they choose to open it, time and space suddenly seem to fall apart. This is likely a case of Never the Selves Shall Meet, but why did it happen for the Reader and not for John after he gained the retcon powers?
If the Reader declines Gamzee's offer of slime pie, he'll decide to stop eating them himself. They worry that this was a mistake- and Gamzee's face darkens until most of his face is pitch-black and the orange of his eyes stands out- and zap forward in time, hearing nothing but some kind of thumping sound when they do, which is described as sounding like someone's head being banged against something. They go forward some more and find the hive is even more of a mess, and the TV screen is broken. The music also changes to "Midnight Calliope", and anyone who remembers when it played in Homestuck will realise what this means. They teleport to Karkat's hive to warn him, only to find that Gamzee's already been there, as shown by the red blood all over the walls. They're too late for Kanaya too (it's unknown if she became a Rainbow Drinker or if there wasn't enough left of her for that), and then when they zap to Vriska's hive after seeing her messages to Kanaya, Gamzee is waiting there, and he tells the Reader that someone told him to kill everyone, and that they'll meet him soon. He presumably kills them after that.
It could easily be assumed that the person Gamzee is talking about is Doc Scratch or Lord English, but it could also be Ultimate Dirk attempting to change the narrative that the Reader has already messed up.
Even Gamzee's good ending is still unsettling. When he starts talking about the Dark Carnival, the Reader realises they already know something about it, and start to remember Karako, even realising how similar he and Gamzee look. This causes them to realise that something or someone is responsible for their amnesia, and end up zapping to some sort of tunnel with a light at the end, and a realistic-looking silhouette of someone, before ending up back at Gamzee's hive. Then they start to forget again.
In Vriska's route, at one point during the FLARP game, she attempts to mind-control the Reader, only for them to fall asleep instead. They have a dream where they see Boldir, who claims to just be part of their imagination, and the Reader remembers her and all their other friends. Boldir tells them how their powers could be used to change many things and asks what they will do. As she says this, strings appear around her and she gets more tangled in them before the Reader finds themself at Doc Scratch's place again, where he claims not to know anything about what just happened.
When the Reader wakes up at Vriska's hive, they see her feeding some of the trolls they were playing against to her Lusus. If they decide to try and stop her, she'll feed them to her as well.
During Equius' route, if the MSPA Reader decides to talk to him about them both being freaks, they'll eventually ask what happened to his horn. Not wanting to listen to him ramble on about it, they decide to go back in time to when he broke it, only to end up witnessing at least three different ways that it happened at the same time. They're lucky to be able to zap back to the present, though Equius now remembers they were there when it happened, thinks they were messing around when they asked him about it, and sends them away.
If the Reader decides to tell him about their powers and demonstrate them, he asks them to take him to Nepeta, only to end up back at his hive. On the second try, the tunnel from Gamzee's route with the figure at the end of it can briefly be seen, and then appears more clearly on the third try, with some text outside of a narration box saying "Quit fucking trying to skip ahead. It's not going to work." After this, Equius somehow knows that this has something to do with the narrative, and it's unclear if this ties in with his aspect of Void, or is the result of something or someone affecting his mind.
Terezi's route begins with her knocking out the MSPA Reader without them even seeing her approaching, tying them to a chair, and acting out a trial where she says their crime is "3X1ST1NG" due to them being an alien.
If the Reader tries to break free and escape, they'll break the chair but still be tangled in the ropes enough to trip and crash into Terezi and fall out of the window, where she somehow gets her noose around her neck, leading to her being hanged while the Reader clings to her body, likely to die from falling if they let go.
The ending where the Reader takes her to Gamzee's hive to distract her from her issues comes off as this when you remember their Blackrom relationship in Homestuck. She even takes off her pants and is shown wearing the same underwear. Granted, this is before Gamzee went through a few years' worth of Sanity Slippage, but the thought is still more than a little unsettling. Good thing it was the bad ending...
In Tavros' route, if the MSPA Reader decides to help his dream self wake up, there is a brief moment as he does so where screen glitches for no apparent reason.
The part in Aradia's route where she reveals herself as a ghost when the MSPA Reader asks about them can be quite unsettling, enough to make the Reader run away. It's somewhat negated when it's revealed she's actually her post-Sgrub god tier self who was using a dream bubble to appear as her past selves, but it still initially seemed as if she was going to do something terrifying just because the Reader didn't believe ghosts existed.
During one of Aradia's route's paths, the Reader tries to zap back to their friends from Friendsim but can't. In the end, they end up in an area of the Furthest Ring, and though the horrorterror they're near is quite friendly, the whispering noises are still a bit creepy (at least until you find out what's actually being said).
On the other path, the Reader and Aradia make a lot of small but important changes to the timeline, which causes cracks to appear in the sky, only for them to close again. And while it's supposed to be the good ending, the Reader doesn't feel that way, with the end card saying "GOOD END, YOU GUESS..." It appears to be another example of them being forced to play by the narrative's rules.
Nepeta's second bad ending comes from the route where the MSPA Reader accidentally brings Dave and Jade over to her hive. Nepeta's lusus is about to attack the intruders, and if the Reader doesn't come between her and Jade in time, Jade will shoot and kill her, which then causes an angry Nepeta to attack Jade in retaliation. Dave and Jade then run away, and the Reader is unable to find them.
Sollux's route has a moment where he believes everyone on the train they're riding is going to die. He turns out to be wrong, but it's still a reminder of Sollux's visions of death.
If the Reader zaps the two of them away from the train, they'll end up in John's neighbourhood, where Sollux will angrily fly away. So now he has trapped himself not just on another planet, but in another universe.
The fight between Sollux and Eridan in the latter's route escalates into Sollux bringing an entire mall to drop onto the ship. And if the Reader tries to zap with Eridan away from the fight, they'll keep missing him, and at one point he'll accidentally shoot their arm off.
The beginning of Feferi's route has the Reader almost die twice, first from being underwater when they zap to Feferi, and then from the air in the bubble she makes for them starting to run out.
When Feferi gets her lusus to contact someone for information on what to do about Alternia, they end up seeing Karako through a crystal ball that her lusus brings in. But the way he talks brings into question whether he really is Karako or if something or someone else is using his appearance or talking through him. It also brings into question just how old or young he was when he died.
Volume 11 reminds us about the assassination attempts and subliminal messages that Jane has been though. It turns out the MSPA Reader actually ended up at her house a week before she was meant to play Sburb, and she tells them it isn't the first time someone has tried to blow her up with mail. The Reader also notices that Jane finds it much easier to follow the voice instructions on her spoon than they do, most likely because she doesn't notice the additional "instructions" that make them feel uncomfortable.
Jane's second bad ending. It initially looks like it's going to be a good ending because Jane has acknowledged the Reader as a friend, and she's doing something nice for them by letting them choose something for her to bake for them. It even shows an ending card. But it turns out to be a fake-out, because then it goes back to the game, and Jane gives the Reader her tiaratop to look up recipes on. They begin to look for one, but the Condesce takes over their mind while Jane watches in horror (most likely confused at what exactly is going on), and makes them zap to where she is, deciding that with the Reader's power, the two of them will "fix everything". The static noise that plays during this does not help, nor does the way the screen glitches before turning red. The narration also changes to first person, making it even more unsettling.
In Dirk's route, he seems to have enough of a control over the narrative (without even realising it) to prevent the MSPA Reader from attempting to go diving and drown, and from accidentally cutting their fingers off on one of his swords. The images of these things happening briefly show up onscreen. The latter is especially terrifying for how easily the Reader could have gotten hurt simply from not being careful, without even having to make a choice.
, which might be our answer. It seems as if Ultimate Dirk from the Meat part of the epilogues is aware of what's happening, and could be trying to put a stop to it.