As usual, context is everything in communication.
"Males are not females" may be accurate when referring to biological sex, but in the context it is most commonly used (as harassment and as a neoconservative tribal signifier) it is referring to gender, and is roughly equivalent to saying "the gender you have now should match the gender you were assigned at birth, or your gender identity is illegitimate".
It's similar to saying "all lives matter". Of course they do, but the context in which its said indicates that it's an opposition to the explicit statement about black lives mattering, a de-focusing and dismissal. "All lives matter" or "males are not females" are not incorrect statements, but in the vast majority of the times they are used on the internet, they are used to express hatred of a group and the active dismissal of that group's efforts to achieve equal human rights. The context in which they are used makes them hateful. Hiding behind the "but it's scientific fact!" is simply a deflection from the fact that it is an expression of hate in the context in which it is used.
I shouldn't have to explain this, honestly. Please stop acting like a jerk to people online.