So far, flint and bronze spears work fine for me. When a spear is put in a quickslot, the game remembers well where to replace it when it picks it up again. Only exception is when inventory is full, and another item si auto-picked up and takes that quickslot.

Did you remap middle mouse button (the one used to launch the spear)?
Did you deactivate the auto-loot mod (V key)?

What can happen also is that you actually lose a thrown spear, because of a decline, or some misshaped obstacle, and you can't locate the item (in the distance).

you can throw them. You then have to locate it and pick it back up. Any chance this was an accidental throw?

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.

I routinely take out birds with the thrown spear. It would take pretty deliberate action to press down on the mouse wheel. Wasn't thrown, in this case.