I was doing a quick replay of chapter two last night and there were a few things I saw that could be foreshadowing...
MC's dad warns about using condoms a lot while we go around having unprotected anal sex with prostitutes (some of us lol)... Pretty insane mood killer but I wouldn't be surprised to see an STD happen.
Tybalt being an obsessive creep over Jill, might try to force himself on her at some point.
A lot of the characters seem to be on pretty hard drugs, you can see several of them have really bloodshot eyes often (Quinn, Riona, Tommy, Derek) so a drug overdose could happen.
There were some other slightly dark underlying tones I noticed but I can't recall them right now, will try to remember them later.
EDIT - also remembered a couple other things I noticed which I wanted to ask about actually. Firstly there's a scene with Jacob when you're about to fuck Sage at the DIK party, where he says that Chad will find out before morning, and starts to mention someone else but gets cut off by the MC (this isn't the first time this happens). Has anyone worked out who Jacob is referring to here? Also when Jade is throwing things at the start of Chapter three she throws a photo of Tybalt. Is Jade Tybalts mother?
For Jacob, it's implied that Sage has some kind of hookup or influence with Burke and the School board during Chad's conversation with her after he gets punished for jumping the MC. Chad says that 'they' will listen to Sage, and Sage agrees to speak up on his behalf, though she warns him that not much may come of it. That may just be because Sage is the president of HOT and as such has a line to the school board, but it may mean something more as well.
Jade being Tybalt's mother is the most likely reason she has a picture of him in her house, but I don't know if we have an actual solid link between them confirming that. It's also mentioned that Tybalt's family donates a large sum to B&R every year, which could explain why Burke is on the school board, but it'd be a little odd not to mention that connection before now.
Derek's eyes are most likely from his drinking. I doubt a maggot would be in on Tommy's stash. That said, I could definitely see Derek going in for the drugs once he and the MC are fully initiated into the DIKs, so that could be a potential drama point in the future.
As for the potential bad things coming up, I'm certain STD's will be involved somehow. Maybe the MC's dad has HIV or something equally bad; he wouldn't keep mentioning it if there wasn't some kind of reveal at some point. I don't know if the MC will catch one, but it'd be a pretty interesting twist on the usual 'Fuck a bunch of questionable women raw with zero consequences' shtick if he did.
But really, every girl has potential bad things on the horizon. Jill has Tybalt's stalker behavior, which she seems either unaware of or aware of it but mistaking it for something else. Maya has her father and Quinn, both of whom could wreck her life in different ways. Sage has Chad, and that will probably come to a head sooner rather than later once he learns the MC is 'rooming' with her, assuming you pick that path. I can't see him taking that lying down. Maybe it simmers in the background if you pick a different branch.
Bella has the most ominous foreshadowing so far, but we have no idea what to make of it yet. Josy probably has the least to worry about on a personal level, but her arrival at B&R means she's ended up in the middle of Tommy's and Quinn's scheming with her links to Tommy and Maya. Who knows how that will turn out.
One thing I'm curious about is the point at which we'll have to get serious about pursuing one of the girls exclusively. BaDIK has actually been pretty generous about letting the MC fuck around; Acting Lessons locked you into a route by the second update if I remember correctly, when you chose between Megan and Melissa, and the only change you could make after that was going after Rena instead. Leah also served as a side option. BaDIK by contrast has 5 main girls, one semi-hidden main girl (Quinn), a semi-serious side option (Camilla), and a half dozen other women the MC can interact with (Riona, the HOTs girls, the strippers). Given how DPC has expressed some rather
heated opinions on harem routes before, I imagine this giant ball of casual fucking is going to collapse in on itself at some point, and Episode 4 might be where we have to start actually deciding who the MC ends up with.