If you are trying to uncheck the option, "Category may contain products" and the system is not letting you, it means that in this category, you have products within that category (thus conflicting with this check box option). We need to move all items in this category out of it.
Under your Inventory tab, you need to find the affected category and move all items out of it to other sub-categories.
In some cases, you may have 100s of products in a parent category.
Another way to move products out of those categories is to do the following:
Within the inventory tab, select the category that you are wanting to uncheck.
Export that to a csv
You will be taken to a file reports tab (on the top right hand corner of your admin, Notifications > Generated Reports )
Download and open the report.
Anything under the Category column that is named after the affected Category that you are trying to uncheck the option for are the affected products that need to be moved.
For more information, please reach out to a member of the support team.