Systems and methods for container analysis and tracking. A method includes scanning a plurality of items by a first data processing system to generate x-ray image data of the items, each of the plurality of items having a unique identifier. The method includes performing a computer implemented image recognition process on the x-ray image data to identify the items. The method includes interactively reviewing the x-ray image data with a human operator by a second data processing system, including displaying the x-ray image data to the human operator. The method includes recording the result of the human operator's review. The method includes determining, for each item, if the results from the computer implemented image recognition process and interactive review meet criteria for items that are exceptions that should not be shipped, and storing an exception indicator for each item using the respective unique identifier.