I don’t think Alya just stopped Lila for the sake of her ship happening. I think she was also trying to stop Lila from making herself look bad. Think about it - Alya is under the impression that Marinette is jealous of Lila and that Lila is after Adrien. So even though Lila was going to Marinette for “innocuous” reasons, Marinette would think that Lila was purposefully annoying her, and thus make her like her less. Alya, therefore, stops Lila to give Marinette less ammunition to dislike her.
But then, what if the other classmates got in on it? Like they genuinely try to help Lila from making herself look bad, inadvertently sabotaging her schemes?
Lila tries to slip in the test answers into Marinette’s backpack? Rose catches her with the backpack before she can set Marinette up, insists that she can take it back to Marinette, and they don’t have to say anything about Lila. After all, we don’t want Marinette getting the wrong idea, do we?
Lila can’t make a class picnic and wants to reschedule? Well, Marinette might think that Lila’s just trying to set up extra work for her, so what if they just hold a picnic for Lila outside of school? We wouldn’t want to stress out Marinette with scheduling conflicts, would we?
Lila tries to pull Adrien away from hanging out with Marinette so she can study with him? Max intervenes and volunteers to help instead. After all, he has some of the best grades in the class and could use the extra time tutoring. We wouldn’t want Marinette to be sad about having her time with Adrien interrupted, would we?
Scheme after scheme is foiled, all thanks to her annoying classmates’ “kindness”. Surely, they have to be scheming to stop her, right? No can actually be that nice, right? But no, they’re all under the impression that they’re truly helping Lila down the line.
All the while, Marinette has no idea about any of this happening, so Lila goes to confront her about it. Some of the girls catch Lila stalking Marinette, and just as Lila decides to start throwing threats, they catch her in the act, saying that they were only trying to help her and Marinette lose the animosity towards each other, and that Marinette had nothing to do with it.
Lila realizes then and there she messed up bad.
Adrien is the one to orchestrate all of this. He tells Marinette not to go after Lila and just leave her be, but doesn't tell her about his plan so she can remain innocent. He goes to Adrien and Alya to argue Marinette's case and suggest coaching Lila so she doesn't come off as trying to rub Mari the wrong way, all the while unaware of Adrien's real intentions. After some convincing, they take the plan to the rest of the class and Operation: Make Lila and Marinette Friends. Optionally, Kagami and Luka are the only ones in on Adrien's real end goal.