You are misunderstanding one key point, perhaps because English is not your first language.
When a customer chooses “arrived too late,” the customer is not disputing that the item arrived. The customer is not necessarily even claiming that the item was delivered outside the expected delivery window.
Instead, it is often selected as a reason by a customer to say that for the customer’s purposes, it came too late. I know it’s a fine distinction, but it is one of the limited number of choices that Amazon supplies in the menu of reasons for return.
As everyone has pointed out upthread, whatever the customer selects as their reason, if the item qualifies for return, you must approve it.