Looking back on the first few chapters, if you want an explanation or attribution for why Aya disappeared, the most likely clue we've got is the bell tied to Aya's left wrist. She's wearing it from the very first panel we see her in, with it having a "ding" sound effect to draw your attention to it, when she reappears it's announced with more dings, and she's continued wearing it all the way up to the most recent chapter. I'm not confident in what kind of cultural signifier that is and looking it up online is useless (like most searches these days ughhhh), but there's no way it's not important.
Also we see Erika in chapter 8 actually writing a Tanabata for Aya to come back, but she calls it absurd while doing so. Not sure she's even remembered doing it, because the far bigger absurdity in front of her lol. It certainly wasn't on her mind at the start of chapter 2, where she seems very openly baffled by seeing Aya, having to confirm with Koto that that really happened.
I really don't think this story has any sort of villain, nor any sort of actual culpability. Just three people with flaws and traits, trying to do their best.