Tell your friend (boyfriend's friend?) that he's annoying you and you want him to stop. If he's a decent person, he'll listen to you. If he doesn't, just walk away from the conversation when he brings it up. You may also want to discuss the situation with your boyfriend, as it sounds like he's the one who didn't want to tell people about your relationship.

(Small side note: Some of your language here really rubs me the wrong way, maybe you could refer to your boyfriend as a closeted trans man instead? Right now it reads to me like you perceive your boyfriend as female/a woman, which strikes me as really really misgendering, something which is super hurtful to a lot of trans people.)

I think it's just annoying, but actually if your friend thinks you are lesbian, this is not really your problem.

You are just friends with a bf with the body of a woman but with the persona of a man. So what. If an other friend thinks now you are lesbian, and he judge negative about you, he's not a real friend.

It could be also the other friend believes you are lesbian but doesn't hate lesbians at all. Oh well, than he could be stiil a good friend for the rest.

That's a difference between just an assuming and an assuming + judgement.