It is easier to understand how they messed up the order of Trump's box when you consider the volume of material and the complex way Trump's boxes had to be handled:
4. Location of Classified Documents Within Each Box
Since the boxes were seized and stored, appropriate personnel have had access to the boxes for several reasons, including to comply with orders issued by this Court in the civil proceedings noted above, for investigative purposes, and to facilitate the defendants' review of the boxes. The inventories and scans created during the civil proceedings were later produced in discovery in this criminal case. Because these inventories and scans were created close in time to the seizure of the documents, they are the best evidence available of the order the documents were in when seized. That said, there are some boxes where the order of items within that box is not the same as in the associated scans.3 There are several possible explanations, including the above-described instances in which the boxes were accessed, as well as the size and shape of certain items in the boxes possibly leading to movement of items. For example, the boxes contain items smaller than standard paper such as index cards, books, and stationary, which shift easily when the boxes are carried, especially because many of the boxes are not full. . . .
3 The Government acknowledges that this is inconsistent with what Government counsel previously understood and represented to the Court. See, e.g., 4/12/24 Hearing Tr. at 65 (Government responding to the Court's question of whether the boxes were "in their original, intact form as seized" by stating "[t]hey are, with one exception; and that is that the classified documents have been removed and placeholders have been put in the documents").
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Plus, it's worth noting which box Woodward {Nauta's attorney] is focused on, A-15. That box happens to have, easily, the biggest number of classified documents in it, 32; a third of the items originally in the box were marked classified. And probably 11 of them, those marked Confidential, have since been declassified and provided in unclassified discovery.
In total, the FBI seized 77 documents with classification markings from the 12 boxes that were seized from the Storage Room, but of those 77 documents, 26 have now been produced in unclassified discovery.