I think there was one person who mistook Jun for a guy once. Called them a hunk, too, which I don't think is fitting regardless of gender LOLOL. I
could say that people have mistaken them for a woman, but that's kinda built into the story; I can't blame readers for believing what they're told. In-universe, they're mistaken for a man and woman all the time.
Angelo's gotten mistaken for a girl once or twice. This happens to him in-universe too, so it's kind of intentional.
Someone mistook Mai for a guy once. Weirdly, in-universe, this happened more to her in her teens, when she had longer hair (doodle at the top for reference)
Not much of a character, but this in-universe Vocaloid stand-in guy design got mistaken for a girl once.
I've always really liked androgynous designs, so it gives me a weird sense of pride knowing some of my character designs throw some people off.