Here's what is _supposed_ to happen with perishable goods:
https://sellercentral.amazon.com/gp/help/external/G201003420...tldr; Anything perishable is supposed to have several expiration date labels on it in large format, and nothing can be sent into Amazon that expires within 90 days. Amazon says they will dispose of anything received with less than 90 days remaining before it expires.
There are a number of things that could be going wrong here. I operate a supply chain company which works with 3rd party sellers, so I'll focus on what I'm exposed to.
One issue could be Amazon's labeling requirements. They actually require a separate label in MM-DD-YYYY format to be affixed to each product. This sounds good on paper, but in reality it means the seller or sometimes a 3rd party warehouse can put whatever they want on the label. Generally, sellers are honest about this, but mistakes do happen and Amazon doesn't necessarily verify what these labels say.
Beyond that, commingling can compound the issue. Say you have 5 businesses selling the same product, and one of them is fudging their expiration dates. It becomes fairly difficult to track down which seller is fudging the dates. This is one reason I recommend all my customers not commingle their inventory (it's an option the seller can choose).
Supply chains can also have wildly varying temperatures. Many sellers choose to work with climate controlled warehouses, but don't consider the trucks used to move their inventory aren't climate controlled. It's highly possible a product meant to be stored at 70F will sit in a 110F truck for 3 days before being checked in at Amazon.