Trans

If the friend was confused because the gender expression or body looked like "she" and the trans man hadn't introduced himself beforehand, then it was just a mistake. It's not crazy that someone accidentally misgender based on gender perceptions, we all gender people in our heads based on what we see and hear, but that doesn't mean it's always 100% accurate.

So the answer to "how was I supposed to know" is: you don't, unless you ask or are corrected. You can ask, but without further clues I also think it can be OK to assume someone's gender, we all do it all the time, and it's OK to make an honest mistake like that sometimes, as long as you're willing to respect someone's self-identity once they disclose it, and earnestly try to use the pronouns they provide.

If they want more resources on this, it might be helpful to point them to the Gender Dysphoria Bible for some 101 level info, and Julia Serano's books, particularly Whipping Girl and Sexed Up, for more exploration of gender and trans identity.

You need to tell him not to get defensive.

This confused my friend, apparently, and he said "How was I supposed to know when he looks so feminine?"

If he is new to queer spaces and is trying to understand than the first thing is to listen, decanter himself and calm down. If for example he called his friend Jason by the name Tyler, would he instantly say "How could I know? you look like a Jason!* or would he say correct to Tyler and carry on.

I understand hee is trying to be an positive, but before he can get to that step he has to learn how not to be a negative, and being upset that someone isn't gendered enough to be unclockable is just feeding fire to the most common trans anexity. He's human, we all make mistakes, he's not bad, wrong or instantly a bigot for assuming wrong. But he does become those things when he begins to argue.

I'm not trying to be hard on him, honest kudos for the effort, but he needs to work on not lashing out at anyone who made him self-conscious. Just gotta correct yourself and move on. Every single trans person would rather just be correctly gendered the next time instead of making an event out of it.