This question already has an answer here:
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)