i purchrased nice boy from slaver marked, and decided to make him girl :), so  firstly in laboratory i added him vagina..and it didnt changed him to futa..but hmm, ok, ok...but even not removing his balls and penis didnt changed him to girls, so here comes "small" problem.

Having boy without balls, penis and with vagina...hmm..ok.

There should be an option in game, maybe with the advanced laboratory or with alchemy that allowed sex change, even if the other changes had to be done separately.

The game has a quest that allows a character to change sex, I don't get why it can't be used for other characters.

Are you using latest version? This should work in 19c at least. 

yes, i have latest version 519c.  and started new game in this version in which it happened.

I also have noticed this same issue. I was trying to change a male aracna into a female by removing all male parts and giving him a vag and it's still showing male and having a male mate with him eventually just caused the aracna to get the homosexual trait. I am also playing 19c. Just for laughs I gave the aracna an amnesa potion and renamed him Nadia Pryce XD. I also just tried making a human female into a male and it still shows it being a female but it says her womb is streil. 

i know something that has always kind of bugged me was the gender icons. i dont know if they are dynamic or not, but to me they should change according to gender.

here is pictures:

this one is futa --

this one is 'female' but the gender icon still says she is futa.--

Figured out the issue. Fix is on the way.