The sexism would be coming from the people collecting fossils and curating the museums. Later in the article they mention that human biases affect the gender ratios of collections of extant organisms (although not for sexist reasons) so it's not a completely absurd thing to rule out.
That theory is excluded earlier in the article: If you’re lucky enough to have a whole bone, such as a skull, the size, shape, and dimensions might differ between male and female. In the case of fragments, researchers might have to dig into DNA
If obvious differences are very rare ("very lucky") then the bias can not come from collectors.
So the argument would be the the (male) paleontologists, museum curators, etc. had such a burning hatred for women that they chose male specimens to cultivate and display?
Please do not flame the discussion with strawmans. This is a very uncharitable interpretation of what OP wrote. It is not about hatred, it is about minor subconscious preferences that if they exist, the can cause noticeable effects in aggregate.
What I wrote is not a strawman, it is the definition of misogyny. Perhaps you are conflating this with sexism. The article used the word misogyny, so that is what I am using.
Explaining the joke to you: Whenever we discover unexpected bias due to sex we usually first assume sexism at work, but that's funny here because ancient megafauna aren't sexist.