Think for gathering purposes you just auto loot the item once the tree, mining node and holes animation finish. I’ve had a lot of times actually where some of the trees or mineral veins are on the edges of mountains/cliffs or by the water and they become unlootable because they “fell out of bounce” and landed somewhere you can’t loot it.
Possibly aswell as you get the higher tier tools(Silver being the highest atm during the EA) if you gather older resources(Copper, Pine, etc) you get more resources.