Consider those who wanted to destroy the documentary evidence, a cabinet level official would not himself hand-deliver bags to a furnace, so he might instruct a subordinate. The subordinate might not be told the contents for obvious reasons. The bags might've been carelessly treated.
The high official does not want his fingerprints on this business so he delegated the destruction of documents in such a way that even the delegation is not traceable and, when not traceable, not so easily supervised or controlled.
He may have ordered it put in a room, thinking it would automatically be burned, but he was ignorant of the actual mechanics of burning documents and so simply succeeded in storing everything for later discovery in the wrong room.
Everyone in the chain of destroying documents who was knowledgeable of their damning contents would be equally anxious to avoid leaving their fingerprints behind. Thus, the opportunities for missteps compound.
Finally, government efficiency only exists when matters are done by the numbers, deviation from the ordinary course, such as would be necessary to hide tracks, might well result in a banal miscarriage of mischief.
Your description of the situation is certainly plausible and well reasoned. The other possibility is that the docs were left behind to be found. I hope you are correct.