I think the most sensible response is that the glass eye belongs to the Other dude with the eye patch, who seemed to die when one of the castaways (can't remember who) pushed him between the sonic pilings. Then he shows up later and explains that they were only set to stun, even though he was bleeding from the ears (???) Why he would leave his glass eye behind I have no idea. Unless he had to leave in a hurry. Do we know if the smoke monster chases the Others too? Because we don't know for certain that the Others control the smoke monster, right?