I agree - they are belittling her, over and over, and always it's people associated with Holmes. But she never calls him out on it and he's never apologized that we know of. I don't know which is more offensive to me, that he considers such gendered slurs acceptable (along with monitoring her menstruation) or that she just takes it. We know he can stop it with a word because now that she's his mentee, it has stopped.

I also considered it a perfect example of the producer's idea of "humor", as Joan continues to be the butt of other gendered slurs, like the "lady with a crazy story" line.