Wikipedia categories are lists maintained by people by adding a line at the end of an article one at a time. Categories can be part of categories and therefore you can have one for Paleontologists and one for Women paleontologists. In order to be a female paleontologist, you have to be in both categories..
Wikidata knows about categories, females and paleontologists. With Reasonator you will find information about all three including what Wikidata expects to find in the category of Paleontologists and Women paleontologists. The number of entries are not the same; a human with an occupation of paleontologist who is female will make it into the list presented by the Reasonator.
The case for categories is a simple one. It is the place where we harvest data from for Wikidata. Until we have something better, it is the place where we will have to come back to.