Yes, it's common enough to be "normal"
When something can be conspiracy or cock up, it's almost invariable cock up.
And the amount of stuff that has been lost (in all sorts of departments) at times like moves to a new building and transfer of paper records to fiche (later scanned) or computer based systems is huge.
What we don't know is what sort of instruction the secretary of state was issuing. Was it "you look in to this" (just to get it off his desk, because it wasn't apparently important enough), or a genuine instruction to investigate. Or a Sir Humphrey moment where you say something that is actually beyond reproach, but leads inevitably to long grass.
The registry procedures and eventual filing could vary depending on which of those (or other possibilities I've missed) it might have been.
I hope investigators are looking closely at where the document went next, and which officials were involved. Even closely held documents would have been seen by a number of people and all their recollections need to be checked.