Amazon has the right to refuse to accept any shipment delivered to an Amazon fulfillment center, but your container is more likely to be turned away if it does not adhere to Amazon labeling, patlletization, and safety specifications.
Yes. Amazon has the right to reject an FCL container if the warehouse determines anything has been done incorrectly (e.g. inconsistent paperwork or incorrect palletization). If your container gets rejected, the trucker will obtain a signed rejection letter, as well as pictures of the offending aspect of the shipment.* Your container will then return to the warehouse where any necessary adjustments can be made, and stored until the next delivery appointment. Each day of storage will incur a storage fee.
*Amazon reserves the right to reject a container without stating a reason. Even if your shipment is perfectly palletized and labeled, Amazon can reject it. If your container is rejected without reason it will return to the warehouse and stored until Flexport can make another delivery appointment and attempt delivery of the container again.