since logan is basically dubbed as a "feral" mutant (he has heightened smell and hearing, inspired by wolverines, believes himself to be an animal to make himself smaller, etc.) i think he probably communicates a lot through body language, rather than his facial expressions or words, and i think the rest of the x men didnt pick up on it until he was long welcomed into the team
he'll stand in front of people he wants to protect, or who he cares a lot about and worries that they might get hurt; he'll tense up and puff out his chest when he gets into verbal fights with scott or the professor or anyone else he may come into contact with, but if they say something that really hurts him, he'll hunch over, point his chin at his chest, overall try to make himself smaller; he subconsciously reads other people's body language to get an idea of the mood and tone of the conversation or how their day has been, and when someone is particularly edgy, he'll tense up with them.
when the x men discover this, they realize that they really have to watch their own body language to ensure that logan doesn't pick up a bad mood from somebody else and lash out/internalize it, and that they also have to read his body language to understand his feelings