Kurloz Makara
Red Death
I think I mistook Cheren as a girl when he was first revealed.
Also, Bugsy and Yellow
I don't remember a lot of these, but I think I could agree to the Tate and Liza thing. I figured they were a pair of sisters as well. I actually think I got a pass on Bugsy and Harley because I read about them before actually seeing them. Bugsy in one of Tracey West's novelizations of anime episodes, and Harley in Dogasu's episode reviews.
What I do remember happening is mistaken assumptions on certain pokémons' genders in the video games. Some people tend to assume pokémon as male by default if they don't take a hard look at at their gender on the card or whatever. I have memories of my cousin referring to my female lotad as "he", and I actually assumed a female electrike I caught was male in Sapphire. Cue my hurriedly rushing to the Name Rater to change "Sparky"'s name to "Sparka". At least electrike are caught right by Slateport, so he was real close, right?
Definitely Bugsy. I was so convinced Bugsy was a girl until the recent advent of the internet.
Whenever the coro coro issue revealed small pictures of Nate and Hugh on the cover, many of the forum users mistook Nate as the female player and Hugh as the male character instead of the rival.
I think I mistook Cheren as a girl when he was first revealed.
Never, I swear. I'm very good at telling genders for some reason.
I honestly never got why people thought Bugsy was a girl. IMO Pokemon has always made the stereotypically assumption that girls hated bugs with Misty being its spokesperson. I even remember one Bug Catcher asking "why girls don't like bugs?". I guess there was that one dude in Petalburg Forest that said bugs would make them very popularr with the ladies, but I'm sure they added that to make the guy sound like a clueless loser. Therefore, it never made sense to me for them to add a female Bug-type gym leader. Sure, there are definitely girl trainers with bug Pokemon (e.g. the twins in Budsy's gym), but they don't LOVE bugs, do they?