They both really like each other while believing the other can't possibly like them back. Mitsuki has been a loner and an introvert all her life, and doesn't want to confess because she doesn't want to risk losing Aya, her first really friend since she was a kid, and thinks Aya isn't romantically interested in her anymore after finding out she wasn't a guy. Aya also doesn't want to risk losing Mitsuki by letting her know she's still in love with her, even after finding out she wasn't a guy. They really just need to tell each other how they feel and stop dancing around it in an effort to avoid getting hurt because all that's doing is hurting anyway.
idk to me it kinda seems like mitsuki doesnt like(romantically) aya as much as aya likes her maybe im just too dense cause i always saw them like aya is head over heels while koga pretty much just has a little crush on her that she didnt even notice yet