Mitsuki's clothing choices so far seem tied to cool music (specifically, middle-aged geezer music) being her life, similarly to her uncle. Andro clothes are cool, black color is cool, rings and piercings are cool, uncle's tattoos are cool, etc. The bio also states that "she's just a girl who loves music".
Aya's feeling stupid for not recognizing Mitiski, guilt at misgendering her, embarrassment at realizing she was gushing to her friends about someone who was sitting right there the whole time, etc
It's on Mitsuki for not clearing up the misunderstanding in time (she wanted to but didn't due to the fear of standing out in any way at school and accidental flirting) and then intentionally pretending to be onii-san because Aya became her music friend and Mitsuki's self-worth was too low to consider somebody wanting to be friends with a "gloomy loner" like her. Aya got angry with her for that.
Everybody else also reads Mitsuki's masked andro look as male (probably due to some cultural expectation that girls will be cute and wear girly stuff, and not being able to go by her face), so she wouldn't feel stupid for it (she has to correct her family on that, too). And while she noticed similarities between Mitsuki and onii-san after interacting with both, she "knew" they're different people and by then Mitsuki was actively hiding they're the same person (you usually don't go suspecting your classmates of leading a double life).
If she's not embarrassed over the explicit issue of talking about her oshi to her oshi, the earlier thoughts about couples and acting like a girlfriend may have thrown her back to confused gay panic whenever Mitsuki is being handsome.