Hi.
Prestashop stores basic product information in two tables. ps_product and ps_product_shop. It is necessary to check which table does not have the three products and delete them in the other one.
When you hover your mouse over the missing product, you will see the product url link and the product id in it. You can also give us a link to the page where the problem is.
Then we can give you a sql query that will remove the problematic products.