When an item will despawn, that means it will be removed from the map if it is left untouched for a certain length of time (if you pick up an item, it will no longer despawn, even if you drop it back where it was.) This behavior was implemented for some items in an unknown version both to encourage automation with workerbots and because some items have more production than consumption, saving you from having to incinerate items in order to keep your map clean of towers of items.

Items currently being despawned Edit

Item Despawn Time (Seconds) Explanation
StoneIcon Stone 120 Stone is harvested alongside metal ore. While both are used for many items, metal ore being transformed into metal has many more applications.
TreeSeedIcon Tree Seed 120 Tree seeds are used to plant more trees and drop when a tree is harvested. While it is useful in the beginning to have more tree seeds than logs, eventually they fill up every storage container possible and bots have no place to put the seeds.
DungIcon Dung 60 Dung is used to make fertiliser. While there are many uses for fertiliser, if one prefers to only harvest the milk from cows, the excess fertiliser would pile up if it did not despawn.