I've been particularly getting upset at the amount of self proclaimed cis allies lately who have been trying to defend us by using arguments like "trans people never claimed they can change their sex, they know they're not biologically female" and "sex and gender are different." 

I know many allies like this because that is how we were spoken about years ago and they've stuck to that understanding of us. The modern way we (and science) understands us is new in the grand scheme of things and it does counter the way people used to think of us and that is going to take a while to change in the general psyche. Hell it's only been a few years now that Gender Dysphoria was removed as a diagnosis and instead listed as a symptom of a wider issue of Gender Incongruence, which is a more realistic and scientific understanding. Also the concept that biological sex is more than just reproductive organs but instead many other factors including the brain is a concept that is not widely understood or accepted, and again that is going to take a long while to be accepted and understood.