From everything that I have read and heard, the problem lies in both the ignorance and assumption of the members.
Many men are unknowingly and trustingly indoctrinated into society cultures that assumes that their organization is the only legitimate one. They are mistaken.
These same men also believe that their practice is the only legitimate practice. Here too they are mistaken.
Unfortunately, in playing both out, they are sucked so far down the rabbit hole of these two fallacies that they attack anyone who dares contradict with facts. This is a shame since in doing so, they inevitably sabotage the very intent of what the Society tries to Cultivate -- incivility, inconsideration, misunderstanding, and intolerance are but a few things that manifest though their blind devotion to a fabricated idol.
Fact: Legitimacy is established by a whole bunch of rules that help regulate the franchise nature of specific Freemasonic orders. It is fabricated!
Fact: Legitimacy is based upon a lot of fallacies that assume the fabricated lore is Factual.
Fact: A lot of Freemasonic Lore is fun, thought-provoking and intentionally entertaining, but some is not Factual.
Fact: Since every last one of these Freemasonic Societies is a Total-Immersion Live-Action Alternative-Reality Role-Playing Theatrical Society, each makes up their own rules and Acts According to those Rules, all designed to protect the interest of that society. This includes all the dogma put forth to reinforce protective natures.
Fact: Both Female Craft and Co-masonic Craft as a whole have no collective interest in attending Male Craft Lodges to co-mingle during Male Craft Lodge activities. In other words, they could not care less. (As an aside, I understand that they would like to be respected for what they Practice, but this respect is not necessary since they shall continue to Practice no matter what attitudes, biases and bigotries they may encounter.)