Mistaking characters for the opposite gender...

Bugsy. Azalea City Gym Leader. I... still don't know. Partly for the non-ordinary name, partly for the hairstyle and fashion sense. If I watched the Pokémon anime it would probably be more obvious, but I don't, so... yeah.

On that note, Tate and Liza. I'm guessing Tate is male, but that's mostly by contrast to the more obviously female Liza. I mean, what is Tate short for? Tathan? Not a name I've ever heard.

I'm sure I've thought similar things like your Yugioh example, boy character whose age still gives them less-manly (adolescent or full-grown man, that is) facial features and a high voice probably acted by a woman. The hairstyle and detailed eyes (I notice a tendency anime that women tend to have bigger and more glimmery irises) also lend themselves to the ambiguity. Still, no other specifics come to mind, so I'm going to stick with Bugsy and Tate.

 

Tachibana Hotaru. She's a girl, but she pretends she's a guy for almost the entirety of the series to fit in with her team. It's happened more than once I just forgot she was actually female...

 

I know someone who's name is Christopher and he's called Tate.

Nagisa Shiota, from Assassination Classroom

Depending on his hairstyle and the situation/artist, he looks a lot like a girl. He also get's crossdressed several times by his classmates

 

Well, most definitely Kirino from Inazuma Eleven Go!

I mean, I still think of him as a her... He does NOT look like a guy to me. Her voice (his -_-) could belong to both a guy and a girl... It's really weird XD

 

I don't know the name, but i know of one character that pretended to be a female under orders, and even forced themselves mentally to fit that role that i was surprised when they were almosr neutered. Until that episode, i thought for sure they were female, thoughso did all the characters. Tate and Liza, i was confused by Tate as well. I haven't seen enough anime I guess for others to come to mind. But usually I can guess the gender fairly easily even in cases where they appear to be a different one.

 

This. When I first watched the anime I actually thought he was a girl for the first 6 episodes. He looks better wearing female clothes too >_>

 

When I first saw this topic, I honestly couldn't think of anybody. But after playing Naruto for about an hour, I realized I forgot someone who fits this description perfectly.
Haku.

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There's a scene where even Naruto mistakes him for a girl in Part 1 of the anime.
I still can't see him as a boy, especially with his hair and voice being the way that they are.

Another one would be Juuzou from Tokyo Ghoul. At first, I was a bit conflicted, but it was all mainly because of the hair.

Spoiler

His psycho-happy mood also played a part in it, I guess.
But I can see him as a guy now without a problem (and a very powerful one at that). In the end, he became either my favorite or 2nd favorite CCG character from Tokyo Ghoul.

 

As sanctuary, i mistaked haku as a girl. She really looks like a girl, oh sorry! I mean he really looks like a girl and his voice also sounds like a girl but he is boy.

 

(Not anime/manga, but still relevant.)
A year or two ago I had a very counterproductive argument with a young relative of mine as to whether Marth as he appears in Super Smash Bros. Brawl is male or female. And yes, I was arguing that Marth is a guy.

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I still don't think we've settled that one...

 

I don't often mistake character's sex, since I have seen enough traps in Anime already.
Notable examples are Kinoshita Hideyoshi from Baka to Test to Shoukanjuu

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Kobayashi Yoshio from Ranpo Kitan: Game of Laplace

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and Shidou Mariya from Maria✝Holic

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China and France from Hetalia

France is really girly

China has his hair in a ponytail, who wouldn't make that mistake?