Hello, I noticed two problems with stockpiles. One is an old thing that always happened in my games: job change items are never put in a stockpile if you change the default settings; i mean: if you select only some of the categories to be stored there those items will be left around and never stocked (none of the categories work for them), even if you check “all” again they are still not stocked and you need a fresh default stockpile.
The second thing never happened to me before: I created a small default stockpile (to store job change items, but that’s not the point), and sometimes my townfolks go there in large groups and just move the items placed around… picking and dropping always in that small stockpile. After a while they eventually get bored and move on.
I hope it is understandable enough.
EDIT: I noticed that when someone is idle he tends to do it a lot. For example I removed my farms for excess of food, and now my farmer spends all day moving around objects in that 3x3 square.