This is happening to me several times now. When moving a lot of items in my stash I often experience a partial rolleback. So after leaving the stash and opening it again several Items got warped back to their old position.
Conflicts in position usually result in those items that should occupy the place now to be in the character inventory (even tough that was empty when closing the stash) or sometimes vanish at all.
Quite often when Items got moved back and forth they even show up in both the stash tab and in the character inventory as duplicates.
The item system seems to be robust enough to ensure those duplicates as well as vanished items to be sorted out on logging out and back in. So I dont actually lose items or gain copies.
Still the whole process of sorting items has to start over, and if this happens I’d better not sell items before logging in and out as the game seems to be confused between the item displayed in my inventory and the actual reference used. I could move items from my character inventory to the stash and on drop into the stash they appeared to transform, so for example i moved an exalted ivory ring from my inventory, but in my stash it arrived as Aboreal Circuit (which was vanished up until this point).