Not sure if this is the issue, but it's something I forget all the time, even after working on the site for YEARS.
Click on the top-level category in your store backend so you are seeing all the products in it.
Then look just a little diagonally to the right of where you see the name of that category above all the products. In blue bold underlined letters, it says PRODUCTS. Just to the right it reads CATEGORIES. Click on that CATEGORIES and your sub-categories should show up.
But also, it's been taking a while (days even) for products to show up after being sorted to a new category. They aren't moving instantly at the moment.
