When you choose the list price for your book, it is a recommended, or suggested price, for the retailer to sell the book for. A book retailer, like Amazon, buys your book from a book distributor at the wholesale price, which is fixed by you the author. The difference between the wholesale price Amazon buy the book for, and the list price they sell it for, is the profit that Amazon make on each book sale.
Once Amazon has purchased stock of your book they can in theory sell it for any price they choose. They may sometimes advertise that a book is for sale at a 10% discount of the list price. They wouldn’t typically want to sell your book for less than the wholesale price as they would lose money on the sale. But they may even do this occassionally when they have stock clearouts to make way in their warehouses for new titles. Because Amazon always buys the book at the wholesale price, and your royalties are calculated from the wholesale price, your author royalties are not affected by the price Amazon sells your book for.
Other retailers also sell books on Amazon, which can include new copies of a book and also second hand copies they may have. The price of these books can vary greatly, and is determined by simply what that retailer wishes to sell the book for. Even though these second hand books may be selling for less than the wholesale price, they must have been bought originally at the wholesale price and you would have earned the normal royalty on that original book sale.
For more discussion of pricing your book, please see our blog article How to price your book.