There is one piece of evidence that incriminates the Alphas:
dildos !
They are the same from the start. The Alphas throw them through the windows of the DIK house, then the DIK pick them up and later throw them at the Alphas house. And finally we find them everywhere in the ransacked house of the DIK.
If it's not the Alphas, it takes a little too much planning and manpower to be plausible.
We tend to create and / or see mysteries where there are none.
For example, Zoey hugging Neil, that's okay with me, and I don't think it's hiding anything.
Maybe it's the same with Bella's bathroom.
But it's true that DPC does some things on purpose. For example the photo frames in the dispute between Jade and Stephen.
Bella's Room is not a created mystery and i believe it's resolved without being resolved my working theory is that bella had a relationship with Jills Sister sheltering her when ran away from home. Inside the locked room is Jills sister's room. I think something happened between Bella's husband and Jill's sister resulting in her drinking and driving/suiciding. Maybe she Adultered with Bella's husband or Bella herself. Bella freaked out and accidently drove her to suicide or drove her to go out on a night drinking and driving resulting in her death. Or if Bella was the cheater which im more leaning towards but there are contradicting hints ill cover them at end. This is when Bella changed her emotions to try to make herself unapproachable and unattractive to people to redeem herself.
So A Bella cheated with Jills Sister and her husband found out Bella broken hearted shut down allianated Jill's sister/her new lover because she was heart broken over lose of her husband.
B Her Husband Diddled Jill's sister Bella found out freaked out her husband left and Jill's sister Suicided/traffic accident/drug abuse take your pick how she died we just know she's dead.
The Evidence for A is Jills bedroom scene "It's not happening again is it?" <This could be a leading for option B as well.
The evidence for B Bellas sex scene in library bedroom. <You've become what you hate.. You're and adultress..(Crazy eyes, broken by MC's hug.)
Also I think the reason why either way Jill doesn't want this to happen is because Her sister Died though Student Teacher Relationships which is also what she's Raising awareness for with those phone calls.
She's trying to make people aware of the dangers of student teacher relationships and might end up being one of the main antogonist against your's and Bella's relationship.
Evidence against it being a sex dungeon which was my first Go To is I think Jill knows whats behind that door. She just seems surprized it was locked when MC mentioned it. Thinking it's probably a guest room aka her sisters bedroom after the runaway.
But this of course is just a theory and it could just be a sex dungeon because Bella's kinky as shit.