I think Aya said onii-san simply because Mitsuki was in her shop clerk getup that initially fooled Aya. She was reminiscing about how awkward she was back then compared to Kanna and Joe.
My guess is more that Aya doesn't think of herself as gay and, at least on a physical level, is more atracted to Mitsuki's casual look, so when she thinks about her in a romantic way, she tends to revert back to thinking of her in the context of "Onii-san", or at least that part of her persona, even though she now knows Mitsuki is "Onii-san" and she likes her for more than just her looks. So, in this chapter, while she was watching the adults flirt, she thought it would be nice if she could do the same with Mitsuki, but when asked she absentmindedly blurted out the wrong name, because that was the context she was thinking in.
I definitely don't think this is true. Aya is certainly attracted to the more butch elements of Mitsuki but that doesn't make one straight. I don't think Aya has any illusions about Mitsuki, she just referred to "onii-san" because she was reminiscing about when they didn't really know each other. She doesn't even seem to be dwelling on it like Mitsuki is, based on the phone call, so I bet the answer to Mitsuki's question of "does Aya still see us as different people" will be an emphatic "No, of course not!"
I didn't say Aya is straight—that seems rather unlikely at this point—but that doesn't mean she's fully internalized that realization yet and drawing a(n increasingly faint) line between Mitsuki in her everyday appearance and "Onii-san" could help ease the cognitive dissonance that causes.
Saying she was just reminiscing doesn't really feel right, both because she used future tense "I[ woul]d never be able to", not "I wasn't able to", and because of the way she panicked and ran after she realized what she said.
but THAT IS THE ISSUE! is way Mitsuki asked Aya if she is nice to her for only the moment when she is “Onii-san” because she DOES feel like Aya is drawing an line between Mitsuki and the moment when she is supposed “Onii-san” while Mitsuki said she is just herself, she ain’t trying to not be Koga and suddenly some one she cares keeps make the “Onii-san” idea to many time so ofc Mitsuki feels like Aya care more about that imaginary person and not Mitsuki, there is quite an distinction that got made by Aya with the whole “Onii-san” and Mitsuki, even i think Aya is taking the “distinction” too far even tho Mitsuki is Mitsuki AND NOT Mitsuki and “Onii-san”
I don't think Aya actually views them as separate people. The issue is that she hasn't been terribly clear about that and Mitsuki can't see inside her head, so comments about being able to talk to "Onii-san" create a lot of doubt and uncertainty for her. In other words, the problem is less Aya thinking there's a real difference between the two parts of Mitsuki's persona and more that they need to communicate with each other better (and maybe take a moment to better explore and understand their own feelings).