A Bill of Entry is a declaration, and a declaration is only as good as the documents behind it. When one is rejected it is rarely because of anything exotic. It is because the invoice, the packing list and the bill of lading disagree with each other on one of four things: the description of the goods, the quantity, the weight, or the value.
Customs does not have to reconcile those for you. If the packing list says 480 cartons and the bill of lading says 476, someone is going to ask why, and the file stops until they get an answer.
The fix is unglamorous: reconcile the three documents before you file, not after. That is a twenty-minute job at the desk and a five-day job at the port.