Until 3.8.6, I haven't had any issues with the category module.
Here's a caveat, though. Before there was the ability to have a single product in multiple categories, you could only have a product in a single category. That category was chosen on the main product detail page in the store management section.
HOWEVER... now that you can have a single product in multiple categories, the category choice on the main product screen (where you upload the main picture for the product is no longer used. It has been depreciated.
NOW, you must click on the "Categories" menu choice at the top, and put the item into the categories from there. Once again, the category choice on the main product setup screen is ignored. Only the categories under the category tab/menu choice are the ones used.
If you have NOT put your products into the categories THERE (they are checkboxes instead of a drop-down), your items, by default, will show up in all categories. This is by design; it's better to show the customers SOMETHING than a blank screen, or a message saying "This category is empty."