There are situations where a single SKU sold on Amazon can produce two or more identical FBM listings on the offer page. One of those FBM offers will be fully controlled via the Inventory screen on Amazon Seller Central and will work deduct stock levels properly. Whereas the other one will just stay there with unchanged stock levels - allowing buyers to keep buying this product despite the SKU being out of stock in the Seller Central.
These listings are called "ghost" listings or "phantom" listings on Amazon. As far as we know, the solution to this problem is deleting the SKU from the Amazon inventory and then adding it back.
For more information on this and maybe new and better solutions to this problem, please refer to Amazon Seller Central forums and general search on Google for the following keywords: Amazon ghost listings.