Firstly, I would highly recommend upgrading to 8 or 9, as the Ecommerce is much more sound in these versions.
Otherwise, one issue can be is if there is any of the products in a person's cart, it may not delete it when the bundle is created as it needs that reference.
Also make sure that you're looking at the Product sku table, and not the order sku. Order skus exist to keep data for existing orders, so even if you delete a product, the "Order sku" of it will remain.
To remove it though, you could use the CMS Loader Module to add an Object Delete hook, check if the object is a product bundle, then perform additional deletes in code.