I recently paid for a hosted server on apex hosting to play with my friends.
We noticed that if items dropped on the ground, there is a chance that it will change in some way and not stack with other items of the exact same type.

I've noticed this as well. A work-around is to drop both stacks on the ground. They'll be able to combine when they get back into your inventory.

That doesn't work very well in mob farms, because going through a whole stack dropping setup is tedious