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Yes, you do have to pay for book overruns up to 10% of your ordered quantity when you self publish a book. If, for example, you order 200 books, and 210 or 220 books are shipped, you must pay for the extra 10 or 20 books. The reason is that book printers cannot estimate spoilage in the printing press process exactly.
According to the custom, a 10% book overrun or a 10% book underrun counts as a complete job. You get charged for a book overrun and credited for a book underrun. If you absolutely must have a minimum quantity of self published books, then the spoilage factor doubles to 20% on the plus side. If your minimum is 200 books, for example, then you must accept an overrun of up to 240.