I use spears a lot and this never happened to me.
What often happens to me is that when i throw a spear during the fight (and my inventory is full) a slot in inventory where my spear was opens up so i automatically pick up some material from the ground and there is no more room for my spear to automatically pick it up.
Since my spear is always in hotbar, its easy to spot that it was replaced with something else. But if you keep your spear in other part of inventory you might not be able to spot it in time and you actually lost it.