Magento – Automatically set product “in stock” after credit memo

Check your system configuration for values set at different store/website levels that might override your global settings.

Check your individual products for configuration that might override your system configuration levels.

Try setting a quantity to 1, purchasing a product, and checking is things are marked out of stock. (i.e. the products you see may have been explicitly set to be in stock with a quantity of 0 before you made your change. If this is the case and the system is otherwise behaving, I'd try setting those products to be out of stock manually)

If you allow backorders (Allow qty Below 0), the setting 'Stock Availability' will not be set to Out of Stock once the product reaches qty = 0