I've also been having some issues with items that seem to exist and not exist at the same time. I thought it might perhaps be related to this. Mine didn't go anywhere near the trade depot though.
I have a raw fish that was caught by my fisherman, but he was interruped before he got it to the relevant stockpile. Now none of my haulers seem to want to touch it, and giving a 'prepare raw fish' order in the fishery tells me that there are no raw fish. It's been sitting there for several seasons now and it hasn't rotted. I can see it, but the game treats it as if it doesn't exist.
I also have a log that I chopped down right at the start of my fortress. It too didn't get moved into a stockpile, and now if I try to build something made out of wood in the tile right next to it, it tells me that the nearest log of that type is 86 tiles distant.
And a possible third case, I have a plump helmet that was harvested from my farm, but then immediately dropped. I haven't quite confirmed whether this item is truly bugged, or if my dwarves are merely slacking, since it happened quite recently (last season).
In all of these cases it seems that the problem arises when a hauling task is interruped in some way. I can see the item, and I can examine it with 'k', but none of my dwarves will interact with it in any way. Perhaps the items aren't being removed from the hauling tasks properly when the task is cancelled? Then the dwarves would forever treat the items as if they were already occupied.