Male characters using "female" names and vice-versa

Probably ignorance and culture differences. I remember in third grade there was a boy in my class who was from Russia and his nickname was Sasha. It was only later that I’d find out that here in the US, Sasha is considered a female only nickname, even though it’s origin is Russian, where apparently it can be used for either gender. I’m just glad the guy never got teased. (That I know of.) 

You could suggest that the translator change it to Camille which is a name for both males and females. 

Abe no Seimei is actually within the standard Japanese naming system. His name is written as 安倍晴明 Abe Seimei. The particle 'no' is a possessive particle, similar to 'of' in English. So Abe no Seimei is similar enough to the name Friedrich von Schmidt or Christophe du Martine.

That being said, there were many people with more than two-word names. For example, in Nobunaga's time, everyone samurai of noble birth may have long names. Nobunaga's name himself was several characters-long, which included his father's name, his generation name, his clan name, his clan's position title and his ancestry. Supposedly, you're not even allowed to call him Nobunaga, people outside his circle were supposed to call him his other name, which Ai-chan can't remember. Those shouldn't be made example though, as although their names were long, those were courtesies to honor their bloodline and station, not really their own names. 

Some names are unisex from where they are originating with slight difference in pronunciation at best. And the most funniest variants... Is losing it after double transliteration.

For example in Russia name like Manuel can be female but Manuil would likely not. 

I’m aware. That’s why I said it was a functional word. But it is a third word. I assume that if he was born in the modern day, his name would be Abe Seimei. So when and why did it go from being okay to have the “no” to not being okay? 

In Russian, Sasha is short-hand for Alexander. Alex(s)ander → shortened Sanya → diminutive Sasha, don't ask me how this works. Female variant Alexandra is also shortened to Sasha.

In US, Sasha and Alexander are different names altogether.

Same with Natalia → Natasha (diminutive variant is also used in US on it's own), Tatiana → Tanya, Alexey → Alex, Vladimir → Volodia → Vova, Sviatoslav/Viacheslav/Rostislav/Yaroslav/Vladislav → Slava (there are so many variants of this name). 

Technically he still can be called Abe no Seimei and his name would be still TWO word name. The difference in writting doesn't change the real name, like at all. 

Probably the translator knows that. 

Actually, I don't see a problem, sometimes male having female name and vice versa sounds good depending on the character and his position 

It is not really the name in normal sense... Because Fujiwara no Mokou means, for example, Mokou of Fuijwara clan. The name would be Fujiwara Mokou. 

yeah... there's not really much research that seems to go into the names for other nationalities, as far as genders are concerned. oddly, there's only a few female characters that may suffer from a male name, while 4/5 of the male cast are either misnamed or almost their entire character is directly plagiarized from famous celebs. it's a little odd, since you'd think even a quick "common (insert country name here) male names" search would clear that up, but, i suppose that could just be censorship at work. heaven forbid they learn about people called abraham, martin, and john. (hmmm... perhaps those weren't the best examples ) 

In elementary school, there was a boy in my class named Allison.  When we crossed paths again in high school, he had a new name.  I didn't really react to it because, many Asian kids changed their names.  It wasn't until many years later that I learned that "Allison" was actually a girl's name.  I figured his parents didn't know any better, but he got tired of the confusion.