There are some scenarios where the products that should not display due to the fact that they are unavailable are displayed on the screen, this happens because sometimes the system miss or even there are no notifications from the broadcaster system to the search module, this happens with the stock notifications that consequently doesn't trigger a new indexation.

Go to a store, and as soon as it updates it's possible to see some products that shouldn't be returned displaying on the screen, even when they are correctly set, this happens due to a lack of notifications from the broadcaster, when you update the products it has the expected behavior.

Reindex the products with issues.