On my shop page, I have category images showing. When you click a category, you see the subcategory images.
For example, I have a category "Bakery" and inside are 3 subcategories. However, the site only shows two of them. Inside the third, there are products that are all in stock and published. But when on Bakery shop page, the subcategory does not show!
I think this also has to do with another issue: I have the amount of products inside a category showing beside the category name. For a lot of categories, the number is incorrect. For example I have over 20 products inside my Alcoholic Drinks category, but it says there's only 1 inside.... Strange!